When you modify a BP file, do you see changes in the browser? Or do the files revert to the original state instantly after closing them in a code editor? What are the file permission settings for the BP plugin files?
What files do you modify and with what changes?
Are you hitting update for the plugin? Plugin updates always overwrite local changes as new files are written over the old ones (unless you juggle with write-permissions for the files).
It is not a BuddyPress issue by itself (tried it myself and I could hack the plugin files just fine). It could be the server giving you the illusion of write-allowed files whilst keeping the files unchanged ("reverting"). Or then the plugins are updated constantly, undoing your changes.
The proper way to make modifications is to either use hooks in a plugin or a theme, or copy over the BuddyPress templates to your theme and make modifications there.