Spotlight will not index ALL folders

Mac OS Extended. Like I said, Spotlight worked on about 10 our of thirteen folders. I just can't get it to work on all folders. Some folders have a lot of subfolders/files. As many as 6000 in one. Don't know if that makes a difference?

Also want to add that my M2 Mac Mini has not played well with any of my external hard drives. Drives go to sleep after a minute or two when computer is on regardless of energy settings. They awaken spontaneously when computer is asleep. This has been an issue noted elsewhere in this forum. Many are having to use Amphetamine keep drive alive to get work done. Also don't know if that's relevant.

Thank you so much for your replies! I have looked in info and folders all say read & write, although I have not redone permissions. Since sometimes the folders will re-index and sometime not, and indexing one folder made another folder, which was previously working with Spotlight, not work anymore, could permissions be an issue?

Addendum: I can open a subfolder, many of which have tagged files. Searching the folder cannot find these tags. I can right click (Control click) and open a tag dialog box and look at the tags, close it without modifying it and Spotlight can then find that tagged item both in the subfolder search and in the enclosing folder search. It's like Spotlight re-indexes the files if I open the tag window or perhaps doesn't look at the Spotlight index until I "force" it to do so. Does not work, however, when I open a get info window and look at the tags.

Also, I can add a test folder to the folders that do not work with Spotlight and Spotlight can find the new folders as well as any tagged items I place in it! It still is unable to find any folders or files that were not newly created or recently had their tags examined.

Addendum 2: just discovered I can highlight the name of a folder, not change anything except copy their name and then Spotlight can find that folder, but nothing inside. I can change the name of items inside folder, change them back to their original, and then Spotlight can also find them! Perplexing!

I haven't heard anything from anyone, so decided to experiment myself. I connected the Toshiba external drive to my Intel iMac, running Ventura 13.3 to see if Spotlight worked any differently than it did on Mac Mini M2 Pro. Same folders could not be searched. I then once again, re-indexed the drive via System Settings and afterward the exact same folders would not search. Makes me think something is wrong with those particular folders. I was planning to try to re-index via Terminal next, but if something is wrong with folders, not sure it would work? I have no idea how to figure out what the problem is with the folders and any help would be greatly appreciated!

After multiple hours of trying to trouble shoot Spotlight not indexing external drives correctly, and after purchasing a new drive and cloning affected drive to it and re-indexing new drive with no improvement, I finally gave up and contacted Apple Support to be told that Spotlight and external drives are a known issue and that engineers are aware and working on it.

Have found a "partial" fix. I meticulously went through the upper most folders and identified the ones that would not index on a general re-indexing of the drive, added them one by one to Spotlight exclusions in System Settings, removed them one by one and allowed them to index. After finishing all of them, I could then search them as far as I could tell when searching ENTIRE drive, but same items found on that search could not be found if searching ONLY the folder individually!!! Not sure if indexing of these folders will continue to work.

I found somewhere on this forum someone who said Apple had confirmed that an APFS external volume will not keep its Spotlight index. I tried to find it to link it here but was unable to in my limited time this morning. Will try to find and link later.

I have had "file not found" happen many times! Hadn't made the connection. Will check out your link. Thanks so much!