John,
Not quite sure by your last post what you changed and which link stopped working. Did you replace %20 with spaces in your attribute table, and after doing so the link no longer worked in ArcMap? Or did you replace %25 with a space in your URL after you followed your link from the flex popup (if so you need to just remove the 25 after the % sign so it reads as the original %20).
Are you working with the source code for flex, if so I can direct you to where you would need to make the change to make it work.
Regards
Gigzy