The best way to remove any varnish on all eeprom legs is to cover all the legs with a small amount flux and then heat each leg up individually until the solder melts on each leg.
This heating process will break up and varnish and then it can be easily wiped away with alcohol spray and an ear bud.
I have often had problems with VVDI-PROG writing these in-circuit, I do not know why.
Orange-5 is the go to for me on these.
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