Now I must ask if there's any problems coming with that method? Arduino IDE don't change anything in Windows, so it should be ok? Everything works fine, but is there something that should be aware?
Umm, there shouldn't be any issues but you'll end up with a load of unused old files.
It would be better (as has been discussed before), if user libraries can be loaded from user documents locations. Then the old IDE could be deleted, a new one loaded and the user-added libraries would remain.
IDE bundled libraries would be updated with no effect on user libraries.