annotation files that contain only groups imported as annotation and junk sequences

The annotation parser doesn't indicate that an annotation file that contains just group definitions is a valid annotion file, so Jalview also parses it with the fallback PFAM parser and adds junk to the alignment (with no undo allowed!).

try the following:

#alignment
>a
asasas
>b
asasasd

#annotation
JALVIEW_ANNOTATION

SEQ_GROUP \t mygroup \t 1 \t 2 \t -1 a \t b