Quoted from ArcadeBar:
whenever I time out in Sanctuary mode and have partially completed the shots, when I go back into the scoop to bring up the mode select the Sanctuary shots are always erased = it will show the mode light flashing on the playfield as partially completed but any shots I had previously collected in Sanctuary are gone and I have to start over.
Unfortunately can't offer much help on your switch issue, but the above is actually part of the Sanctuary mode rules.. If you don't finish it, you have to start all over to get the completion (although halfway status for II does save). Makes it a stressful challenge for sure!
Rules for sanctuary:
Duration: 68 seconds
Complete all 5 of the Hadron Enforcer targets and the left orbit before time runs out to complete the mode (and score 3 free Hadron Enforcer activations). Note that the Hadron Enforcer itself isn’t available to use in this mode. The upper gates do not divert to the pops, so be ready for a full orbit shot.
Upgrading during this mode will allow flashing targets to be spotted with a shot to the left orbit.
Completing Sanctuary begins Super Targets for 20 shots. A roving light moves around all 5 of the Hadron Enforcer targets. Shoot the flashing target to collect a Super Target award. A hit to a solidly lit target is worth 200k base, while a hit to a flashing target is worth 5x that value.
If the mode times out, you lose progress and have to make all 5 shots again. If you drain before completing the mode, progress is kept. You still get “halfway” credit (for Immolation Initiative) if you made 3 or 4 of the 5 targets.