Whch further evidence have you got since
In general: Modifications by other programs than the player itself are likely to upset the player and depending how it treats the files (e.g write a play counter) this may lead to a damaged file.
If you modify the data from within the player, then the player has full control over the file and probably (provided, it has been programmed in a decent way) will not do any damage.
Why do you ask again?