I'm not sure whether to do a code critique or just ask what problem this script is trying to solve, so I'll offer both.

Code critique:

• There's no POD that explains what this script does.
• You've used good variable names, but there are no comments.
• You silently rename a file (or not) depending on input arguments and your badline count.
• There's no caption on your output.
• There's also no shebang line at the beginning of your script, and you don't need either the exit or the __END__ at the end of your script.
• You should really use standardized indention -- I highly recommend perltidy for this task.

Object critique: MD5 sums are a great way to get a 'fingerprint' for a bunch of files -- it's very handy to confirm whether two files on disparate systems are the same. It's not clear whether this utility is working in that direction or not; there's no clear explanation of what the inputs and outputs are.

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