It may be a little reassuring and make the tedious work not easier, but I regularly have to deactivate the more than 1700 entries and reactivate them step by step to detect any incompatibility. Despite everything and as you said, sometimes FS remains quite complicated Good luck finding the troublemaker quickly. Just as a suggestion: use an easy handling scenery tool, like FS Scenery Manager. It's much easier than any default solution.
Bernard