My 2 cents.
Note my opinion here may be a bit biased, because I don't use Ubuntu, but here is some wise advice.
I have multiple installations.
in my experience with IDE I have found that the following can happen with ANY IDE.
In the event something breaks, nothing has changed, I just remove the offending install.
If I have a package that doesn't install the "normal" way, for example PJRC is the notable offender here. I wish Paul would fix this and make life easier. There are less disruptive ways to do this.
Last is if I purposely modify something on my own for my own use, which is rare, but happens.
So, I suggest that it does not upgrade in-place, but rather update in parallel, in a new directory, with a separate icon for each version.
Many other IDE packages operate this way, most notably Netbeans. I have 3 different versions of Netbeans installed, each with a different capabilities. Sometimes a plugin isn't updated on Netbeans, and you get stuck. I totally dislike eclipse and do not use it, but I assume the same happens there too. I would be surprised if it didn't.