This is a not so intuitive, but designed feature of unison. Quoting
v2.9.20's changelog: 

"Restarting update detection from the graphical UI will reload the current
profile (which in particular will reset the -path preference, in case it has
been narrowed by using the "Recheck unsynchronized items" command)."

The 'r' key shortcut, which is equivalent to the 'restart' feature in the
'Synchronization' menu, triggers that behaviour.

The really bizarre part is that the 'restart' button in the toolbar does not
trigger that behaviour. --path' preferences are kept while roots are
compared again. I plan to notify this upstream when the time is right
(meaning: when they are done dealing with other submissions on my part).




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