Per group colours shaded by consensus and thresholded with Colour by Annotation colouring not restored from Jalview Proect

1. Import a protein sequence alignment
2. apply Taylor + Consensus shading
3. Compute a tree and partition it to define a few subgroups.
4. Apply 'Colour by annotation' using the Conservation annotation row, check the 'Use existing colours' option, and set a threshold of 'Below' and the slider to 9.
5. Hit OK to apply the colourscheme.

Create a new view, or alternatively save as a project file and restore. Groups are now shaded with single colours - and certainly not the same as the original alignment view.