To help with testing, I recommend what I oftentimes do to test my code. Copy the actual file you load into your code as $file_to_check to a new subdirectory. In there, run a copy of your script against copies of the copy and/or making a mock version of the file -- bang! Instant Clean testing!

You can even trim the code copy down to just the bits that you're worried about, esp. if the code does other things, as well. That's something that reference to Perl Testing: A Developer's Notebook will help school you in, so I second davorg's wise recommendation in that area.

Also, in your loop, I would personally recommend, on top of ikegami's rewrite, that you drop out of the while loop with a last before you delete. You do need to close the file first, and having that close be outside the loop will make it easier for others to read now, and likely avoid some issues in the future.