"Insufficient Permission for Setup Progress" message just after Login

I replaced two files that were corrected, deleted .pyc files in folders, restarted bench. .pyc. files were regenerated, however, I am still getting the same message.
Should I do anything else? Is there any bench command that would refresh all files involved? I am in production mode (with developer_mode = 1 in config_site. json), and bench update is not an option dues merge conflicts…
EDIT: not sure if it is correct, however,

bench migrate

did trick to me.