Hi Marcel,
I don't know German at all so I may have missed a few things but from what I can see, there are a few elements that may be causing this.
Your .nl site has the stronger link profile with 197 referring domains and a Domain Rating of 48 compared to 36 referring domains and a Domain Rating of 37 for the .be site.
As you pointed out, the two sites are almost exact duplicates of each other as well. Unless I'm missing something, there is nothing to mitigate this duplication so Google is typically going to rank the strongest of the two duplicates and almost ignore the other.
So, for the question of why you were seeing the .ne site ranking before and not .be, I would expect this is because they're both duplicates and .ne was the strongest.
As for why this has reversed now, I can see you've dropped a lot of links and referring domains from the .be domain recently, perhaps this was an intentional removal of low quality backlinks? If so this will have improved the strength of the profile.
On the other hand, the .ne site has picked up a large volume of links recently and only a handful of new referring domains which suggests these new linking domains are very low quality. Since you seem to have lowered the quality of the .ne profile and improved .be, I would expect to see the situation reverse, which is exactly what has happened.
Suggestions to Fix the Problems Assuming I am correct, there are a couple of ways to go about it:
**1. **Use only 1 website instead of 2. I realise they're for difference countries but the two locations are only 90 minutes apart. This could be dealt with by having 2 location pages on the one site. It removes the duplication you're currently struggling with and means you only have to work on a backlink profile and content for one site instead of two.
**2. **Alternatively, if you have a large budget or a lot of time available, you could tidy up those low quality new links to your .ne site and start writing some unique content for one of the domains so they're no longer duplicate.
So long as Google is seeing 2 identical websites, you're never likely to see them both rank well at the same time. Quality signals may go up and down over time which sees them trade rankings, but you're never going to see them both at #1 while they're duplicates of each other.
I hope that helps!