Q1. Do your flights have similar altitude records in goeotags? drop all photos in one project, hit keys 5 (ortho) and then 3 (side view) and see if the blue balls are more or less well placed in terms of altitude, i they are not, you can amend altitudes by export reference inputs (geotags), use excel to fix altitudes by using ground home elevation + flight altitude and import them again into ref pane... then all flights should align without problems with reference checked
Q2. Rather than using two psx projects you should have used separate chunks in same psx. However, you can still merge project by append command under file menu
good luck
GEOBIT