I've been using Perlbrew for a very long time, certainly well in excess of a decade.
Currently on Cygwin for 3-4 years; before that on Mac OS X (later macOS) for 8-9 years;
and other systems before that whose details I don't immediately recall.
I performed many upgrades on those systems and never had to mess with Perlbrew for any of them.
I do not have ~/.perl5. Is that, by any chance, a typo in your post (and should be ~/perl5)?
Here's some of what I have:
$ env | grep BREW | sort
I checked in https://perlbrew.pl/ and noticed the latest version is 0.96.
As you can see above, I have version 0.86.
I then checked in https://perlbrew.pl/Installation.html in case I'd missed some change:
that's still showing ~/perl5; no mention of ~/.perl5.
If you could tell us a bit more about what system you're using, what the upgrade involved,
and why you 'had to "deactivate" perlbrew', we might be able to provide better help.
A package manager (apt, rpm, zypper, etc.) would normally install system Perl modules.
With Perlbrew, you'd use something else (cpan, cpanm, manual 'make' install, etc.).
It would be useful if you described the interaction between your package manager and Perlbrew.