If I Wages of Pain enemy on BF and go in to attack, he flashes to go back to base, does that unit heal from combat cleanup?

Yes, the unit will still heal during the Combat Cleanup, even though it was moved back to base before combat damage could be dealt.

According to the RiftJudge FAQ (ID 8342, 4531, and 3522):

• Combat is initiated the moment a unit moves to an occupied battlefield.
• Once combat is initiated, all steps and phases of combat proceed, including the Combat Cleanup step.
• The Combat Cleanup step triggers healing for all units in play, regardless of whether combat damage was dealt, whether the combat damage step was skipped (e.g., because a unit was moved away), or whether the unit was actually involved in the combat.

The Sequence

1. Initiation: You move your unit to an occupied battlefield. This initiates combat, designating the players as Attacker and Defender.
2. Chain/Reaction: During the resulting Showdown, your opponent plays Wages of Pain and you (or your opponent, depending on the scenario) use Flash to move a unit to base. Per RiftJudge FAQ #10310, the Flash (moving to base) resolves first, potentially making the target for Wages of Pain illegal.
3. Combat Cleanup: Regardless of the Wages of Pain outcome, since combat was initiated, the game proceeds to the Combat Cleanup step.
4. Healing: During the Combat Cleanup, all units in play (including the unit that moved back to base) heal all marked damage.

This is my interpretation based on the mechanics of Combat initiation and the provided FAQs. No official FAQ exists for this exact combination of Wages of Pain and moving during combat, but the principles of combat healing are established.