If there is a world that has Imperial Loyalty but no troops or ships, do it stay loyal or does it go neutral?

Yes as loyalty is only effected by missions.

A subjugated system would loose its subjugation marker if no imperial ground forces where present, but this would not effect loyalty.

It might help to think conceptually about what the two represent:

1) Subjugation is military occupation, with troops forcing the populace to work for the Empire.

2) Loyalty (Rebel or Imperial) is the mood of the populace, working for either side of their own will.

I think one thing that FFG could have emphasised more is the fact that loyalty and subjugation are two completely different animals. Yes they have similiar end results. Yes they interact. BUT, at the end of the day, they are gained and lost in completely different and unrelated manners.

I think one thing that FFG could have emphasised more is the fact that loyalty and subjugation are two completely different animals. Yes they have similiar end results. Yes they interact. BUT, at the end of the day, they are gained and lost in completely different and unrelated manners.

Thus, a planet loyal to the Rebellion, can be subjugated by the Empire, but still remains loyal to the Rebeelion, and will return to Rebel production if Imperial Ground Troops are removed.