Upgraded to MB 5.10.1 and MB AOI 1.30.1 seems to solve the original problem (wiping out the group field entirely anytime perform an update via rwmb_set_meta().)
However, seeing these console errors in WP Admin if there is a group element present on the page/post/user:
Uncaught Error: Syntax error, unrecognized expression: ##type_1:not(.rwmb-clone-template ##type_1)
at I.error (load-scripts.php?c=1&load%5Bchunk_0%5D=jquery-core,jquery-migrate,utils,zxcvbn-async&ver=6.6.1:2:11769)
.
