I would use PitStop Server to process the 300 individual files.
However you could also combine multiple files into a single PDF, run in PitStop Pro, then split back to the original source files (be careful though, you may have issues such as losing PDF-X compliance or perhaps other issues).
The only benefit is that it saves you running the action list 300 times. You have to spend the time combining and splitting… For example you could comine x6 batches of 50 files each, then you only have to run the action list over 6 files. So a poor form of “automation”.
Combining separate PDF files in Acrobat Pro using the Create/Combine Files into a Single PDF command will create Top Level Bookmarks, which can then be used to Split to individual file names. Multiple page PDF files are correctly handled as the Top Level Bookmarks are applied to each page ensuring that all pages are contained in the split.