I\'m pretty sure I\'ve read somewhere that you can actually move the main plugin *.php file to somewhere else (I assume under your theme directory) to have it safe in case you m
Are you talking about running parts of a modified 3rd party plugin, and an updated version, at the same time?
That's not going to be possible. There is no magical method of "preserve my changes and transfer them into the new version automatically". The way to go here is doing a diff between the edited version and the update, and integrating the changes in the actual source files.
The bottom line is, if you manually edit a third party plugin, you're in for manual review (and possibly rework) once an update takes place. That's why it's usually not a good idea to extensively modify third party plugins.
With themes, Wordpress has a concept of "child themes" which allows exactly that: to keep changes separate from main theme, in case it changes.
I haven't yet found a way to do this with plugins.
I'm using a few tactics myself: