We expected to warehouse a pre-seed deal that’s now raising a Series A, though they’ve since pivoted and are now off thesis. Balancing between being on thesis vs. showing early mark ups, on which side should we err?

The VC Lab Assistant is correct in general. If you have already invested in the deal personally, and have created a warehouse policy such as moving the angel investments made in the last 6 months into the fund, then it's ok to move the deal into the fund.

That being said, having a markup on a company that is not on thesis early in the fundraising cycle is not that useful because you will end up speaking about the company a lot post the 1st close during investment pitches. This can cause message confusion, or create questions/doubts/objections that you will need to defend.