Remove gaps / gapped columns doesn't adjust hidden or selected columns

I'm attempting to refine an alignment to create a figure containing just a region of interest, so have many columns of the alignment and some sequences hidden. If I now attempt to remove empty columns, with nothing selected, all columns are removed from the alignment.

The previous attempt at removing empty columns prior to hiding a further sequence showed similar but less dramatic effects, with all columns up to 964 (I think) being removed, some of which are clearly not empty.

I've attached screenshots from before I attempt to remove empty columns (and a matching project), and following removal of 'empty' columns...

It appears possible to work round the issue by filtering by occupancy, although this results in the hidden columns becoming unhidden again