EDIT

this is a remaining issue of 'Move taxonnodes should be available for multiple selection' (#7463#note-29)
Andreas Müller wrote:

The refresh issue still exists and is critical. It seems to happen with large subtrees. E.g. I moved Charyophyllaceae Juss. with all its >>100 children from 1 classification to another. This took some time (percentage was at 100 for longer time before the job really finished, so we should also work on the percentage computation, 100% should not be reached before the save has really finished - save takes long because many tree indexes need to be recomputed).
Using refresh from menu did also not work. Only reopening navigator did solve the problem.

This still happens though it does not happen always. Once the tree is opened at both places it does not happen but at beginning it may happen.