I'm using Pianoteq in a project within my DAW. ... Can someone please tell me what to do to make sure those settings are remembered?

I'm guessing it's not something in the DAW but probably your settings in PT?

If you have not done so already, try in PT Options / MIDI / Global MIDI mapping click the dropdown and select Attach 'pippington's saved MIDI map' to current preset. Otherwise it may switch to a default MIDI map, which sort of sounds like your concern.

I have just discovered a nice way to set up my two foot pedals connected to my Arturia midi keyboard. I'm using the expression pedal for sustain, since Pianoteq can deal with a graduated sustain pedal, and the ordinary cheapo sustain pedal as a simple switch to operate one of the other pedals.

Having shut down the project and come back to it a day later, I opened up Pianoteq and it had forgotten the new pedal settings, even though I had saved it within a Pianoteq preset.

I'm a bit surprised about this.

Can someone please tell me what to do to make sure those settings are remembered?