I apply the Property Frozen Package = Fix to the symbol itself.
This means the user has to renumber the pins and Reference Designator manually, as packager will not do it, but most users prefer this anyway and the Pins and Reference Designator are preserved after updates.
In this case, I usually preassign on the symbol a ref designator of J1001 and manually renumber when placed on the board. An assigned Ref Designator and Frozen Package = Fix are the tags to prevent repackaging and reassignment.
I tested on my testcase, and the pins were not renumbered.
Thanks for the response! Did you rev the symbol? I already have the Frozen Package = FIX on my parts. The instance properties, such as Ref Des are preserved by the Tools > Update Symbol, but I lose all of the assigned values for pin properties.