I have a domain that is set-up with Google Business Apps for email under one Google account, and I verified the domain using a google-site-verification TXT record. BUT, I've just added it to my Webmaster Tools which is under a different Google account, and added a second google-site-verification txt record along side the existing one, as it didn't detect the first TXT record.
Is this safe to do? It has verified ok, but I'm just wondering if it will break.
its perfectly fine.
every google account has it's own google verification hash which you have to put in DNS TXT record, or in meta tag, or as a file, and you can do it multiple times,
BUT
since you alerady have one account authenticated you could simple add another one from domain options in GWT rather than ading another external verification.
You could do the same by adding this account as admin to GA account for this domain.