Is it acceptable to change affiliation to new employer when submitting an updated manuscript when old employer provided limited research support?
I would recommend to use both. If the journal differentiates "address" and "current address", then:


"address" is X (where you did the research)
"current address" is Y (that's where people can reach you now, right?)


If the journal doesn't distinguish them, I would put Y first (you seem to consider Y more important). If the journal doesn't allow two affiliations, them the journal is strange; just try to put both affiliations in the one field and see what happens.