A few points:
- The fact that these servers are Apache servers is moot. This has no bearing on the answer.
- If you don't have SSH access this is going to be impossible to do remotely. You are going to have to download the files, check and modify locally, and then re-upload them.
There is a possibility if you generally know the location of the files that you could write a script using ncftpget/ncftpput to download the files, check and modify them locally, then upload if changed. Depending on how many files and servers you are talking about, this is going to take forever.
I would think a better solution is to install ssh so you actually have administrator access, or if not seriously consider changing your infrastructure to allow administrator access and not just user-level access.
With ssh this would be almost trivial to perform with a small shell script.
Otherwise, buckle up, it's going to be a lot of clicking to fix your files.