Once T180874: Ignore deprecated constraints in constraint tool is implemented and deployed (i. e. soon after group1 moves to wmf.17), we need to do another import of constraints from statements so that deprecated constraints are removed from the wbqc_constraints table. See T169647 and T169200#3459891 for the last time this was done.
Details: The ImportConstraintStatements.php maintenance script needs to be run on Wikidata, which is apparently done with the following shell command:
mwscript extensions/Wikidata/extensions/Constraints/maintenance/ImportConstraintStatements.php --wiki wikidatawiki
This will produce as many lines of output as there are properties, so it might be prudent to redirect the output to some file. It should not take longer than a few minutes.