I've been having this issue as well. I discovered (accidentally) that the locator references are also stored in the individual maps. I happened to get the "Maps" section expanded before the errors started and noticed that the locator errors would come in clusters, then pause. Additional maps would load during each pause,
after which the locator errors resumed.
I came up with a Python script to remove all the disabled locators from each maps definition. The assumption is that if the locator was enabled, it was valid, otherwise it wasn't supported. Of course, this would remove any locators that you manually disabled. So far, it seems to be working. It does not remove the unsupported locators from the project. That needs to be done manually. Be sure to save the project after running the script.
#get current pro project
thisProject = arcpy.mp.ArcGISProject("CURRENT")
#list all map objects
maps = thisProject.listMaps()
#find the "enabled" locators and assume all others aren't supported
#replace locator list with enabled only
for m in maps:
mdef = m.getDefinition('V3')
loclist = mdef.locators
newList = []
for l in loclist:
if l.enabled:
newList.append(l)
mdef.locators = newList
m.setDefinition(mdef)
