When I ported my 14000 pages worth of stuff over from MS Word, I faced the problem of having to choose between capitalized or lowercase versions of my individual – now md extension – files.
Because many files related to persons, geographical areas, etc., I decided to capitalize common nouns/words of filenames as well. This looked weird in my texts though, so I had to run some regex replacements that provided the lowercase versions in aliases ([[Alias|alias]]), while keeping sentence starters and the personal names intact ([[Robert Burns|robert Burns]] or [[Robert Burns|robert burns]] would have been equally weird).
My new file creation Templater template also automatically inserts a lowercase version of the filename as an alias, which can be deleted as I go along if not needed.
So for now, this is how I go about dealing with this. There are indeed a lot of extra characters, which luckily don’t show in (Live Preview and) Reading Mode.
There are some threads on the forum which deal with Obsidian sync where they talk about this problem of handling case differences.
I also chirped in with what I saw in how GitHub Desktop was handling these cases:
So – although I’m far from an expert – it could be a limitation on more than one operating system (and Obsidian must heed all of them) or syncing/file version tool. I had not looked into this more deeply, nor do I intend to.