I was able to find a way to reproduce the problem consistently:
mkdir -p st_test/foo/lvl1/lvl2
mkdir -p st_test/foo-bar/lvl1/lvl2
touch st_test/foo/lvl0.txt st_test/foo/lvl1/lvl1.txt st_test/foo/lvl1/lvl2/lvl2.txt
touch st_test/foo-bar/lvl0.txt st_test/foo-bar/lvl1/lvl1.txt st_test/foo-bar/lvl1/lvl2/lvl2.txt
Add the folder st_test to a new project.
'Reveal in side bar' (RISB) will work for every file in foo-bar, but only for lvl0.txt in foo. When RISB is not working, for instance for file foo/lvl1/lvl1.txt, "File not found in open folders" appears on the status bar.
Rename foo to baz, and RISB works for every file in baz.
Apparently when two folders named like foo and foo-bar exist in the same project, the paths get confused somehow.
This has been a problem only since 3127.