I’ve been noticing this problem many times in the four years I’ve been using Obsidian. And most of the time it’s an annoyance, but tolerable. But yesterday, with the release of Insider Build 1.6.5 I decided to do a complete reindex of my vault in the hopes that that would knock some sense into it, and I’d stop being forced to wait through a reindex of hundreds of files every time I opened it on my Mac. That was a mistake. 
Now I am waiting through the reindex of thousands of files when I opened Obsidian this morning - just like when I forced the reindex yesterday.
My vault has 20,106 files as of right now. And it grows by 10-100 every day.
What I’m trying to do
I am trying to get the reindexing to “stick.” According to the message “this should only happen once.” and it happens every time I open Obsidian ususally indexing the same approximate total number of files. In other words, I open Obsidian on my Mac and it gives me the standard
“Obsidian is indexing your vault… This should only happen once. Some functionality may not be available until this is complete. (0/483)”
The 0 number then increments through getting to usually 10-50 from the final number and the message disappears. I assume that it’s indexed.
I turn off Obsidian (after checking that sync is complete). Turn it on again later or the next day and the message is back, usually with the exact same (0/483) number.
I use Dataview heavily in my vault, so I expect it to need to index a fair amount. But on my Mac it seems like the indexing isn’t actually written to Obsidian’s files. I have no idea how that actually works, and 90% of the time I’m just glad that Obsidian does work as well as it does.
But the line “This should only happen once.” Is irritating. Because for me, it happens every time I open Obsidian. Which is significantly more than ONCE. I know this is stupid, but even if that line were just changed to refer to the interval e.g. This should only happen once [per day/per session/when you reopen Obsidian/etc.] I wouldn’t find it so irritating. But this is a me problem.
Things I have tried
I have tried:
- restarting Obsidian
- rebooting the computer
- updating my OS and the Obsidian installer
- doing absolutely nothing until the entire index is “finished” (today it got to 19268 / 19271 when the window disappeared - closer than usual) - I didn’t touch Obsidian or open any other apps on my Mac until the indexing was done. I just kept jiggling my mouse so that it wouldn’t go to sleep. With 19K files, that’s pretty darn tedious. (And took like 10+ minutes).
- searching for extremely large individual files - The largest .md file I found was 98KB, other than that the largest files are image files. I removed that file from my vault.
- it doesn’t do the repetitive indexing on my mobile devices (iPad and phone). On those devices it just indexes every once in a while, usually if I’ve made a large number of changes on my Mac
- meditation
- whining to my friends and family