I could not reproduce this when I tried to switch around message IDs in References fields in an existing thread. Navigation in the summary always followed the thread order in the summary buffer (with vm-summary-show-threads on).
In another test case, however, adding a 'References' to an otherwise unthreaded message put it into a short 2 message (now 3) thread in the right place (and navigation worked). But when I removed the artificial 'References' header, the message did not lose its thread indentation until I quit the folder and re-entered. Toggling vm-summary-show-threads off then on didn't help. Also note that vm-discard-cached-data did not help here. Does it help your failure case?
I could not reproduce this when I tried to switch around message IDs in References fields in an existing thread. Navigation in the summary always followed the thread order in the summary buffer (with vm-summary- show-threads on).
In another test case, however, adding a 'References' to an otherwise unthreaded message put it into a short 2 message (now 3) thread in the right place (and navigation worked). But when I removed the artificial 'References' header, the message did not lose its thread indentation until I quit the folder and re-entered. Toggling vm-summary- show-threads off then on didn't help. Also note that vm-discard- cached- data did not help here. Does it help your failure case?