It is my practice, and encouraged with my players, to save characters to a file with name and level, so we can back track through changes if needs be.
Normally, File > Save As is just perfect, but it doesn't work when I save the Eidolon of a Summoner (and probably other companion types).
Open Summoner
Open Companion through tab, switch to Eidolon
(Eidolon) File > Save As, new name
the Summoner is marked "modified" and needs saving
File Save Summoner
the Summoner is unchanged (bar the usual unstable entries), and specifically the link to the Eidolon file is not changed.
If i re-order this and do
Open Summoner
Open Companion through tab, switch to Eidolon
(Summoner) File > Save As, new name
File Save (Eidolon)
the Eidolon is saved with a link to the new name of the summoner.
It's trivial, but a pain, to have to edit the save PCG file. My players always forget, and end up with 2 copies, and keep updating the wrong file.
Pathfinder core ruleset