First, it is generally best to either mention Arics Expansion in the title or add this to his thread, as the author will be the most knowledgeable of issues cause by the mod and may not have time to search all the threads. As I believe this case to be barely related to the mod, it is fine.
Second, if you changed the file after a backup was made, but before the mod was applied, then the changes would be erased when the file was replaced with the backup.
Third: using "globals.state.reputation.values()" is an error from vanilla that I had missed, as ".values()" creates an array containing duplicates of the values (dictionary structure is "key : value"). Thus the changes to reputations have no effect on the original array.
The basic resolution would be to use:
for i in globals.state.reputation:
globals.state.reputation[i] -= 10