Indexes defined in "/jcr:system/mode:indexes" don't reflect ModeShape configuration

I've noticed that index definition nodes in "/jcr:system/mode:indexes" accumulate over time: they get created based on ModeShape (XML) configuration but they are not deleted when they're removed from the configuration.

(Should it matter, I've applied patches for MODE-2392 and MODE-2393).

And deleting obsolete index definition nodes in "/jcr:system/mode:indexes" is forbidden, e.g.:

Unable to remove the '/jcr:system/mode:indexes/local-index-provider' node in workspace "default" becasue the node is within the '/jcr:system' area","stacktrace":"javax.jcr.nodetype.ConstraintViolationException: Unable to remove the '/jcr:system/mode:indexes/local-index-provider' node in workspace "default" becasue the node is within the '/jcr:system' area

So what's the proper way to alter index definitions in ModeShape?