To respond, I don't think it was an EMD or PMD (partial matching domain) issue as the domain is not relative to any keywords, industry, etc.
If the 301s are removed from these uppercase urls and sites link to them, would the canonical do enough to inform the crawlers to pick up the lowercase version where the canonical tag points to?
Would this cause link juice to be split between the uppercase urls and lowercase urls, or would the canonical take care of that? Note: there are plenty of links going to the uppercase urls because they were in existence for several years.
Thanks for the other suggestions.