I am trying to transfer my electrum wallet, which was imported from MultiBitHD. I just found out that Electrum is not compatible with other wallets since it doesn't use a BIP39 seed. Can I use my old MultiBitHD wallet words although they have been used for recovery once?
If you are sure the old wallet has not been compromised, you can use the old BIP39 seed again. The seed represents the private key that stores your coins so using it once does not make it invalid since the point is to be able to recover your coins with just the seed.
On the other hand, it shouldn't be too hard to generate a new BIP39 seed that you can use and be sure isn't compromised.
Yes you can as many times as you like. Electrum does support restoring from bip39. It's just that native electrum seeds don't use bip39. Multibit developers actually created a video advising people to migrate to Electrum using their multibit seed.