so this came up the other day: what happens when you make a tzinch lord take a ward save and you have a the OTS. The lord normally has a 3++ and re rolls ward saves of 1. So does he loose the refill of ones and has to still reroll any 3+ he makes, or does he not reroll the 3+ and just loose the reroll ones?

Neither re-roll is lost, but the re-rolled dice for the ward save cannot be re-rolled, regardless of the reason for the first re-roll.

If the Tzeentch Chaos Lord rolls 3 or more on the first attempt to save, he re-rolls due to The Other Trickster's Shard. If he rolls 1 on the first attempt to save, he re-rolls due to Third Eye Of Tzeentch (the relevant gift).

If he rolls 2 on the first attempt to save, or 1 or 2 on the re-rolled save, he takes a wound. If he rolls 3 or more on both attempts to save, or a 1 on the first and then a 3 or more on the second, he saves the wound.

I was under the impression that the core FAQ had ruled that if you have conflicting rerolls, for instance reroll ward saves and OTS, they canceled each other out. My concern would be that the chaos player would argue that since the OTS turned off the reroll of 1s that it would then be spent and not affect the 3++ made wards

The re-rolls do not conflict, because there is no situation where the same result causes a re-roll from both effects. The Other Trickster's Shard only triggers on a successful ward save. Third Eye of Tzeentch only triggers on a ward save roll of 1. Now that the Pendant of Khaeleth is gone, there is never a circumstance where a ward save is successful on a roll of 1.

Neither of these effects "turns off" the other. They're just both subject to the general rule that no dice may be re-rolled more than once. Your opponent can argue that the rules cancel each other out all they like, but this interpretation is incorrect.