I've had similar problems with using .php files.
First of all, I agree with the real Jerry -- don't work with the recovery disk. Copy the PHP files you want to work with to someplace else.
Then, when you need to use them, here's a hack that worked for me:
Bulk rename to all those archived *.php files to *.php.txt (for example, or some other hack that works for you). A .txt file normally won't be executable, no matter what's in it. If they still keep their executable permissions, you can navigate to the directory and run:
chmod 664 ./*.php.txt
... or whatever permissions you want to set.
If you need code highlighting in your text editor, edit your editor's view preferences so such files display just like .php files.
Then, when you actually need to use the files, rename them back to .php. Alternatively, if you're including them into other .php files with an include or require call, you may be able to just include them as named. I've included many files without .php suffixes into .php files, and had all the included text executed as PHP code. YMMV.