Glad you figured it out. I honestly didn't think it would have been the canonicals. I'm a little surprised that the bots didn't just choose not to respect the suggestion as opposed to blanking your site from the index. Didn't think that was even a possibility from incorrect canonicals. Good to know for the future though in case anything like this comes up with anyone else's site.

Not exactly. Its not so much that the canonical "supersedes" an index, follow tag.... a canonical tag establishes equivalency while a NoIndex is more like a "does not equal." The Index, Follow is still there and being seen by bots as they crawl... in fact, if you had NoIndex on a page with a Canonical Tag, it may not even see the canonical at all since you told it to NoIndex the page. The Meta Robots Index tag comes first allowing the bots to crawl and index the page but then the canonical sets up equivalency to a separate page. So if your canonical tag is being respected, it doesn't wind up doing the same thing as a NoIndex (though it may seem that way) nor does it do the same thing as a 301 (though there are similarities in how equity is passed). Since a canonical establishes an equivalency, you'll find that the Canon Page will eventually take the place of the Canonicalized Page in search results because you're telling them the Canonicalized Page _is _the Canon Page & that the Canon page is the right version of both.

I took a look at all of the usual suspects as well... which amounts to pretty much everything that everyone else mentioned but I was intrigued by this issue and thought maybe another set of eyes might notice something that was off. Nothing was wrong in the page source from what I saw, no issues crawling it myself and I didn't see any penalties. Normally I'd think that if your homepage wasn't appearing for branded organic searches then a penalty was levied against you but when that is the case the homepage is still normally find-able in a Site operator search. M__aybe it is related to all the backlinks that were lost/deleted in the past month but I'm not sure why that would be the case unless removing the homepage from the index was a Penguin response to link issues... but I was under the impression that peguin was devaluing the link source not the link recipient and deleting/removing links seems to be a preferred method of handling penguin-related issues. So if there is a relationship between penguin and your homepage being deindexed then I am not sure at all why nor am I certain how to fix it as I'm not seeing anything in particular that screams "linking issue" at me. (though I only did a fairly cursory inspection of things)

So I am stumped. Whenever the issue is figure out I would love to know how/why this came to be.

If a URL was indexed and has since had a canonical added to it pointing to another page, it will eventually disappear from results. Basically the pages gets consolidated with its canon page. If the bots choose to respect the canonical tag in that instance, all signals get passed to the canon page while still allowing the page and information to be accessible by human visitors. As such, there's no reason to keep the page in the index because you're telling the bots that another page is the correct page instead. This is not the same as NoIndexing a page but will eventually remove a page from the index much in the same way that a 301 will pass equity along to another page while eventually removing the redirected page from the index in favor of the page being redirected to.

It is absolutely natural for people to link to your website with your URL. When looking at your backlink profile, you should see tons of links with the anchor text being things like your naked url or "website" or "this". In fact, it would be incredibly unnatural, and potentially a sign of paid linking schemes, if every single link to your website was a keyword rich, long tail anchor.

There is nothing "bad practices" about allowing a non-existent page to 404. People often times forget that a 404 isn't a signal that something is broken and needs fixing, its just a status code that returns "Not Found". Sometimes it makes sense for things not to be found on your site because they were never there in the first place. 404s eventually stop being crawled and indexed.

You shouldn't just bulk redirect things to your homepage though. Its always best to have a 301 point to the most relevant page based on what the original page was. If there is no most relevant page, have you considered 301-ing them to one step up in the site navigation? (i.e. a category page or hub page)

What call tracking platform are you using? Most of them will let you keep you main number (which is likely the GMB #) and continue to show that to the Bots while showing a different phone number to users based off of what groupings you've set up (i.e. one # for organic, one for PPC).

This may help: https://kb.yoast.com/kb/how-do-i-noindex-urls/#group

Are you using any specific seo focused plugins like Yoast or All-in-One SEO? They should have the option to update the Meta Robots tag to NoIndex, Follow.

If your Tag pages are creating duplicate content, you can go back and NoIndex those tag pages & they won't show up as duplicates in the index. It may take some time for Google to recrawl, recognize they are noindex'd and then remove them from the SERPs if they were ranking anywhere.

Personally I think you should set up a process whereby every time a vehicle and/or part is removed, you have someone automatically 301 it to the previous step in the site navigation. So when "blue widget 3" is removed from the site, anyone landing on that page or who has it bookmarked winds up on the "Widget" category page. Now there may not be an easy way to do it right this second because of how many there are now, but if you get in the habit of doing it and slowly work toward fixing the others then you'll be in a good position in the future to keep this from being an issue again.

Now if you really don't want to attempt that... 404s aren't necessarily horrible (too many can be). If your site is properly serving 404s then you won't be penalized for it but in this case you might want to consider using 410 status codes. Its a stronger signal for removal than a 404 and you don't plan on the product ever coming back so marking it Gone should get it removed from the index faster while also helping to keep you from competing against yourself in the SERPs when a new but similar product comes into stock.

You might be better served by using a canonical to point the parameters to the base page. I.E. /shoes?gender=1 with a rel="canonical" pointing at "/shoes". Depends on the variety of the content of the pages, if you're cannibalizing your own keywords, etc.

In my personal life? Hate Live Chat Pop Ups

If i'm on a site browsing or planning out a purchase, the last thing I need is a chat box to pop up multiple times during my visit trying to get me to convert better or speak with a specialist. If I wanted to speak with Cutomer Service, I will click your wonderful Contact Us button. If I wanted to speak live with a person, you have your phone number right there on the page. If i'm trying to do some pre-purchase research or plan out spending, and you pop up a live chat box every time I come to the site and possibly 2 or 3 times a visit on occasion... I will close that box, get frustrated the next time i pops up, and eventually choose to go back to the site less because its the one with that annoying Chat Pop Up.

Now, I completely understand the business reason behind them and how they can help improve customer relations and increase conversions. I'm all for including them on client sites (where sensible) and ensuring they aren't intrusive. I'm just personally not the customer that will convert off of that. You need to find the right balance. If they come up too often, you'll be pushing people away. But if they come up too infrequently, you may have jut lost a customer who needed a bit of help and a small push to finish converting.

This is a very common issue. When you publish a new blog post with tags, and your tag pages are index-able, you are essentially posting the same content to two or more places on your site. The two easiest options are either don't use Tags or make your tag pages Noindex.