After upgrading, all of custom CQ user groups had lost the replication rights it had in 5.4. All other permissions remained.
The replication privileges are lost because of new property that was introduced in CQ 5.5 called crx:replicate.
Attached is a package with a script that fixes the problem. Simply run it BEFORE the upgrade to CQ5.5.
Upload and install this package in package manager on CQ5.4 and to run it go to:
Make sure the Dry run checkbox is unchecked and click the run button