Over the past year three related things happened.
The lihata board format became much more capable than .pcb and became our native file format. Saving a backup now in .pcb does not make too much sense as it potentially leads to data loss.
On the other hand I did not get reports of the lihata save code crashing, not even the complicated code that tries to preserve original formatting, so the .pcb backup did not get too much use.
Finally, I got a bugreport from Ade about composite layers ruined after a while. It traced back to the auto save: saving in the .pcb format has no choice but degrade the board, which then affected the lihata version as well.
So I decided to remove the emergency .pcb save from io_lihata. Now it saves only in the lihata format.
If you want to use subcircuit features, you need to save your board in lihata board v3 or newer.