Many of these can be IBM save files from PTF installation.
When you put on a ptf, SI12345, for example.
And it fixes object IBMPGM in QSYS.
It will first save the original IBMPGM to a save file, let's call it
Now, if you do a RMVPTF it will restore the program from that save file.
If you apply SI12345 permanently it will delete the save file SI12345V1.
If you upgrade your OS prior to applying PTFs permanently on the old
version then SI12345V1 will stay out there for all eternity. I had some
from SEVERAL releases back.
This is why applying your PTFs permanently can be a space saver.
I know you explained how your third party uses save files as fix markers
but the above can also account for many of these.