... If the Fleet Commander's flagship suffers a Bridge Smashed critical hit, any remaining Fleet Commander Re-rolls are lost for the remainder of the battle.
Obviously, re-rolls bought for your admiral are lost if his/her ship suffers a Bridge Smashed result. However, there are other commanders, such as Battlefleet Cadia Captains, Chaos Lords, etc.
A player makes a Chaos list using the 12th Black Crusade list. In this, a Chaos Cruiser has a Chaos Lord embarked, and also has the Mark of Tzeentch. The Mark's description clearly states that the Chaos Lord gains a re-roll. This ship suffers a Bridge Smashed result before the re-roll is used. Can it still be used?
1. Yes. By very strict reading of the rules, only Fleet Commander re-rolls are lost from Bridge Smashed results. The Chaos Lord is not your Fleet Commander, as his re-rolls only work on his ship/squadron.
2. No. Chaos Lords are a part of the 12th Black Crusade list under the category Fleet Commander, and therefore count as (smaller) Fleet Commanders and are subject to the above rule.
3. Yes. Although the idea in option #2 above that the Chaos Lord is a Fleet Commander (just not the main one) is correct, the Mark of Tzeentch is not a Fleet Commander re-roll and therefore is not lost.
I'd say that #2 is the more reasonable.