Comment 13 for bug 1641308

I see a similar problem with incorrect partition information in gnome-disk-utility. I am not sure if it's exactly the same as the OP's issue as in my case the problem is solely triggered by running GParted, and not by the deletion/modification of partitions as mentioned by the OP.

I suspect that GParted is somehow causing udisks2 to report incorrect information. Running "udisksctl info -b /dev/<partition device>" for the extended partition (the one that's incorrectly displayed by gnome-disk-utility) - shows the Block object's Size is 0 instead of 1024 and "IsContainer" value is false instead of true. Rebooting restores the values to be correct.

If the OP is still around and can confirm that udisksctl also shows incorrect partition data in their case, then perhaps this bug would be better assigned to the udisks2 package rather than gnome-disk-utility (there is an upstream bug tracker in Gitlab for the latter in any case).

My testing so far has only been on 16.04; there is a newer udisks2 packaged with 18.04 onwards, so if time permits I'll try and replicate this there too.