Things I have tried
I have used Windows PowerRename to add a vault specific unique suffix to each file within each of the vaults. I also did a search and replace to add that vault specific suffix before each occurrence of ]]. By combining the vaults now, I can be sure that there won’t be any conflicts. But, the situation is not ideal.
What I’m trying to do
If there is a way to combine the notes from multiple vaults into a single folder, without having to individually deal with each duplicate and without having negative consequences and conflicts, I’d be very interested in hearing about it. I only say that it is important to use a single folder because I want to avoid having duplicate note names identified by their path. I have tried using that workflow but have run into strange results when changing note names.
I was going to make a feature request but figured that there is probably a separate tool or workflow that can make this process less painful and risky.
Edit: I just realized that my method causes problems for non .md files whose embeds show their extensions in Obsidian notes. It also causes issues where the link is not simply to a note, like when Liking to headings. Anyways, this realization only makes my help request more needed. Fortunately I made backups!
Thanks for any suggestions.