Pier Tier 1 Map and Alva Temple Portal Trouble... (Oh Bother!)

Alva-Master Explorer incursion 2 of 3 stuck. Alva will not move to third location but stays stuck at 2nd. This came about because I elected to do her Temple while completing Atlas Pier tier 1 map. I "think" I created portal in the Pier to dump items before continuing with Alva's incursions. I thought this was working but I could not return to this portal... Instead I ended up in the Atlas lab and took another map portal back to the map but when I returned to Alva in this same pier map she was no longer interested in the 2 of 3 incursion. I retraced the map and found her 1st location and her at the 2nd location but could not find her third location.

Is this something that will clear on its own once I log off and back on another time or have I somehow ruined Alva's Lost Temple??

During Maps does the portal only return you to the Atlas room where to continue one must use up another 1 of 6 portals?

Regarding Alva, does what happened make any sense as I explained it?

Can Alva pick up the 3 of 3 incursion to the temple in a different map from Pier tier 1--thus there being nothing wrong?

You should have been able to talk to Alva at the 2nd encounter and you can select view temple or enter incursion.
If you gave up it's fine, you lost some rooms, but she will offer new rooms next time.
You can screw it up good so you only need 1 Alva mission in a map to complete temple. I did this last night.
Friendly advice, Never run a temple from a map, if you lose the game and lose the map, you just lost your temple.
Same for Jun, always run from hideout.

TLDR: nothing wrong, she will generate normally the next time you find her, and that can be any map without a master mission. Or you can select her mission by talking to her in your hideout and selecting master mission, then put a map in her map device and she will launch the map and put herself in it.