What happens if i cast sanction to empower Kharox and then cast another sanction to disempower it. Do the end of turn effect of each sanction still trigger?

Yes — both end-of-turn effects still trigger, because each Sanction created its own Delayed Ability that fires on its own schedule regardless of what happened in between (Rule 392).

Casting the second Sanction (mode 2, "Disempower... Empower it at end of turn") does not cancel the first Sanction's pending "Disempower it at end of turn." At the Ending Step both delayed triggers go on the chain. Since you control both, you choose their order (Rule 383.3.d).

• Sanction #1's delayed disempower: if Kharox is already disempowered when it resolves, it does nothing (Rule 442.1.a.1).
• Sanction #2's delayed empower: it will still Empower Kharox at end of turn — and since Kharox is no longer Empowered at that point, this is a new Empower event that retriggers his "When I become Empowered" (Burn 3, then optionally play a unit from their trash).

Ordering matters only for the final state: if Sanction #2's empower resolves last, Kharox ends the turn Empowered; if Sanction #1's disempower resolves last, it removes the status. Note Empowered isn't a "this turn" effect, so whichever empowerment survives the Ending Step carries into the next turn.