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I was looking at php.net for a stripping or converting function. you could try something like htmlspecialchars() it might read them right and the dump them into the DB properly and then if you get them and show them in HTML they might come up right but this is a shot in the dark.
when I got files from a PC I used to run a BBedit script I have to convert the PC chars to Mac but that doesn't really help.
If you have a set of chars that you know are wrong and what they come out as you could parse the files on the way in and use regex to replace them.
As a Mac developer myself, I know that it does depend on your text editor. If you are editing any server scripts you need to use a safe text editor or script editor.
For my Perl scripts, SQL, Java and so on - Adobe GoLive will open any of these and allow for safe editing - without the added zeros and such that your speaking about.
These also are great:
Mac Perl [macperl.org...]
Mac Simple Text by the way is not the best editor on earlier OS 9. But Simple Text for OS X is a good bet.. just make sure to set to plain text and not rich text (RTF) as you know Mac OS X is Unix base (grin) so your scripts should be easier to edit there.
Enjoy and hope this was a help.