@eastcoastelle,
I have some similar anecdotal evidence. I found the Kobo/GoogleDrive feature seems to have limitations that the Kobo/Dropbox feature doesn't have.
In my case I didn't want to create a separate subdirectory for each author but I did want to store every book as 'LN, FN - Title' (because this seems to work well for calibre being able to match them to its library equivalent) and store them in 26 subdirectories, A, B, ..., Z based on 1st char of LN. This worked just fine for Kobo/Dropbox.
However, when I tried to replicate this organisation for Kobo/GoogleDrive I found that each subdirectory could only contain a max. of 100 book files, the rest just "disappeared". I kept the book filenames the same but ended up creating 80 subdirectories (e.g. Aa, Am, Ba, Bark, Be, Bi, ..., Y, Z) to hold them.
I think this GoogleDrive limitation only exists for Kobo because I also use GD to store epubs that I may want to download to my Android phone (if/when Calibre Companion stops working) and the 26 A-Z subdirectories work fine for that. One of the subdirs contains 500+ book files.
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