Should attachments be left on when impressions are made for Invisalign mid-course correction?

Normally , dentists would take the attachments off as teeth have not moved the way they were supposed to. So the new positions could be different. But still they are the best people to determine your exact tooth movement and so devise your treatment plan. So trust them or ask them if in doubt, not the assistant.

Yes a lot of times the attachments are left on the teeth
when new impressions are taken, unless your doctor wants to change their position.
It is also possible for new attachments to be added later.

Odds are strong that the dental office knows what they are doing. If you have doubts, you should talk to them. 

Yes the attachments should be left on.  Presumably the movements you are trying to accomplish are still the same.  Removing the attachments at the time of impression might entail putting them right back on.  Invisalign is aware of what is tooth and what is attachment.  Have faith, stay the course and good luck!!!