Do the pellets in the burn pot have to touch the ignigtor?

on the start up our stove seemed like it did not drop many pellets into the burn pot and it took a really long time to fire up.

I can't remember how full the pot was before.

Just got stove running after auger jam in which we removed as many pellets from the auger as possible. Maybe this had something to do with it.

now I am afraid to take the stove out of T stat mode and put it back into Smartstat in case it won't start again.

No, the pellets do not have to touch the ignitor to start. They are started by having heated air blown into the pot to ignite them.