I'm creating a script to remove the tombstoned entries in WINS (required for exchange w/ multi domains). What I'd like to know is if removing those old entries will break anything? Or if there's anything I should look out for?
No it should not break anything. Tombstoned records in WINS aren't used anyway. According to TechNet:
... The owning WINS server changes the status of selected WINS records
from active to tombstoned in its database. WINS then treats the
records as inactive and released from use. Once these records are
tombstoned locally, the owning WINS server neither responds to nor
resolves NetBIOS name queries for these names from other WINS clients
and WINS servers unless the records are registered again by the WINS
client. The owning WINS server replicates the selected records as
"tombstoned" to other WINS servers during subsequent replication
cycles.
No it should not break anything. Tombstoned records in WINS aren't used anyway. According to TechNet: