Can I re-enter Thailand with ongoing visa application paperwork after leaving for a second time?

I’ve been over the land border twice on visa entry stamps (bus to Myanmar). I’ve now applied for a 12 month Thai language visa, but the paperwork has taken much longer than intended. This means I need to leave and come back into Thailand before I get my paperwork (the paperwork I need to activate the visa). I’ll need to leave a 2nd time after I get back, to activate my language visa.

Will I be able to get back in the 1st time to get my paperwork etc? My language school wrote a letter, and told me I’ll be able to get in... but when I left Thailand today, they told me I would have to get another tourist visa...

Can anyone please confirm