Any chance of pictures? Perhaps damping off. Most likely cause is overwatering. But if the seedlings are literally disappearing rather than keeling over and dying visit them after dark with a flashlight. You might have a slug.

If you're using a heat mat and grow-lights, you're likely growing indoors, and I suspect you won't have any slugs. As such, I'm not sure what "disappearing" means. As in, seriously, the plants are just going away? If they are dying, it would help to see the dead plants to understand why. Damping off is where the plants rot at the lower stem and just keel over. As noted, likely from overwatering. Although you have a heat mat, which keeps the soil warm, the air above better be pretty warm too. Thyme doesn't like cold. 70-85F is optimal.

I get indoor slugs! Not often, but they sometimes come in with plants or make their way in from the garden. That’s life in a damp climate.

Best guess is to much water. It is shocking how often plants need water. Slugs or other creatures would eat some one night, more the next. You would probably notice that.