To confirm I haven't changed any settings for the past 3 weeks, just logged in to see my stacks wiped.
Have checked my settings and the stack multiplier has changed to 'ItemStackSizeMultiplier=2.0' which is unusual for having text in it.
If I revert to a save with the current settings, surely that would wipe over it. I will change it to just a number and revert back to an earlier save, will let you know if it works.
Changing setting back to a numeric value and importing older save worked. Alas, I was in the air at the last backup so fell to my death, but got my tranqs etc back.