Yes, edit orders can be tricky as the orders.php is touched by several mods. Edit Orders and One Page Checkout come to mind. There are others, I'm sure.

The secret is in the merge. Any mod should first be compared with the basic load. We've found many a mod using an old file as their basis for updating. Using something like that with a blind overwrite is failure cause #1. Overwriting a previously merged file with a new file is #2. Kiss of death is the Filezilla Apply to This Transfer selection. I call it the "let me shoot myself in the foot" method.

Just be careful, document your steps, and backup the site and database every time you even think about changing a single character on the site. As Monk said, "You'll thank me later."