Cleaning before using WITH_META_MODE

What cleaning options minimize interference with the use of WITH_META_MODE ?

Occasionally buildworld stops because of a missing dependency, usually
just re-running git pull fixes the problem. In cases where it does not
fix the problem how should one rank the various cleaning commands, from
least to most thorough? Using rm -rf /usr/obj obviously works but AIUI
deletes the data needed by WITH_META_MODE. The cleaning commands I've
used include
make clean
make cleandir run once
make cleandir run twice
rm -rf /usr/obj

but it isn't obvious how they interact with META_MODE.

This is in the context of -current on Raspberry Pi2,-3 and -4
if it matters.

Thanks for reading,

bob prohaska