Does Mournful Witness still empower if it flashes out of combat?

Yes, Mournful Witness will still empower when the combat ends.

"When a combat that I was in ends" uses past tense — it's a historical check. If Mournful Witness had an Attacker or Defender designation at the combat battlefield at any point during that combat (even briefly), then when that particular combat ends, the trigger fires. Moving it to Base via Flash after it already gained its combat designation doesn't erase that it was in the combat.

(Rule 384.2 confirms triggered abilities evaluate while the permanent is on the Board — Base is still the Board, so the trigger can evaluate normally.)

The only way it wouldn't fire is if Mournful Witness was moved away before it ever gained a combat designation (e.g., Flashed out during the cleanup before Attacker/Defender designations were established). Once it's designated as Attacker or Defender, that historical fact is locked in for the rest of the combat.