Have been working on Missouri batch - but returning many due to them being relevant California. Is there a way that I could flag them to be listed under California?
You will have batches that will be from different states. Doesn't matter if it's the Missouri or New York projects. It's been this way since I started in 2015. You'll index the batch just as you would if it took place in Missouri.
The suggestion from @erutherford indeed appears to be the "official" FamilySearch stance, as it has been for many years. However, in practice, it is at complete odds with the general consensus that the purpose of indexing records should be to act as a finding aid in discovering the records of our ancestors, relatives and others.
The same problem has been reported regarding collections relating to different English counties. I, and several others, have reported many thousands of vitals events that took place in County Durham being placed in collections for the county of Northumberland. Likewise with Cumberland records being included in Lancashire collections.
This advice, and practice, should be stopped immediately, as it is causing our relatives' records to be practically impossible to find through FamilySearch. I have reported instances of my relatives being incorrectly indexed with "Northumberland" baptisms, but (even if work on the batch involved was ongoing) I was told there was nothing that would be done to correct this misleading information.
If indexers feel as strongly as I do that researchers should be presented with factual information on the FamilySearch website, I believe they could help prevent researchers being presented with false detail by refusing to index such material - which will be of little or no use once placed online.
To make this issue clear, FamilySearch is currently expecting its users to know that there is a good chance of a relative known to be born in California being indexed as being born in Missouri, just as I am finding (sometimes after several years of searching) my Durham relatives have been recorded with Northumberland baptisms.
In that indexing work on such projects is not achieving the purpose of acting as a finding aid, would indexers please make every effort to stop this practice, which (as illustrated) leads to researchers KNOWINGLY being presented with false information, once these records appear online?