First, gaps stick out like a sore thumb.

Second, with just a little bit of diligence they will easily see you worked there, but didn't list it on your resume. They then have the question of 'Why not list it?' in their mind. Their mind will build a narrative you do not control or influence, and it's not a positive one.

Better to be 100% open and transparent. List it on your resume, and talk to it during the interview 'Due to our CTO leaving I was no longer a fit with their changed culture or mission, so left to seek other opportunities. I did stay in contact with the CTO however, and he can provide a reference if you'd like.'