You mention that the files you are parsing are now appended to rather than being overwritten. It should be possible for you to save the position of your last match for each file every time you do a run. That way you could immediately skip past what had already been parsed in previous runs when starting a new run.

You would probably have to do a check on each file to make sure it hadn't been overwritten, perhaps save the size of each file as well and check that the file is not smaller now than it was during the last run.

Cheers,

JohnGG