1. If you attempt to close SGP at any time and the sequence has not been
saved, you should be presented with a warning asking if you want to save
the sequence. Even if the sequence stops because of clouds, as long as SGP
is not closed you should get that warning dialog. Is SGP somehow closing
after aborting the sequence?
2. Note that Equipment Profiles are completely separate from a sequence
once the new profile-based sequence has been created. If you make changes
to an Equipment Profile it will not make changes to any sequences based on
that profile. I suspect you just mean the control panel settings in your
sequence and not the Equipment Profile, but just wanted to be sure you
understood that distinction.