Here I have >20,000 individual one bar MIDI items loaded in Reaper with drum sequence content:


(Shows as more than one bar per item as I just quickly loaded them without accommodating the tempo ; ), but trust me, based on your description they are pretty much the kinds of files you are working with.)
Then, instead of doing a batch resave, select them all on the track, right click one of them, and do a "Convert active take MIDI to .mid file reference"

This will result in all of the MIDI items being saved individually into the media directory you have specified in Reaper preferences. Effectively batch resaving each and every one of those items into a new file. You can then operate on them further, copy them to a safe place to be stored and reimported and so on.
This takes about six seconds on the system I tried it on
You will probably want to do some management on the file/item names when reimporting into a new project, but batch renaming items is another function that takes mere seconds.
This way you will be able to experiment iterating your clips batch saving them as often you'd like, without waiting hours on end in the mean time.
Remember that immediately after the conversion, the items on the timeline now refer to the newly generated .mid files, so don't get burned by that in some way (changing the references in this manner in an ongoing project and habitually saving it that way, then moving the files away, etc).
