Apparently, it seems I've found a good solution to my problem. I'll
explain it here, in case someone have the same problem as mine.
I noticed that the problem was always the same : the modification that
couldn't be performed was always the same. The name of the project (of the
Method Plug-in) couldn't be changed.
So I just had the idea to load the Method Plugin again (the instanciated
project), after the instanciation, and then just change the name (because
changing a name has never caused any problem).
And then, I have my project with the removed features and the correct name
I wanted it to have.