I'll post this regardless of your answer for future reference:
On windows, paste this into a new text file:
Code:
@echo off
for /r . %%f in (*.epub) do <command>
and replace <command> with whatever command you want to run. Save with extension .bat in directory containing epubs, run from command line.
This will recurse through all subdirectories and run the command on all epubs it finds. If you only want to check/fix the ones in the current directory, use this instead:
Code:
@echo off
for %%f in (*.epub) do <command>