They'd likely have no issue with a 3rd entry since they aren't maxing the first 2 stays, but certainly applying for a tourist visa after getting the 2 exempt entries would be an easier and cheaper solution for that.
PERIOD OF STAY: How long you can stay on aforementioned visa.
The visa has a specific period in which you need to use it for entry, and allows a certain period of stay once used. Your stay starts on the day of entry, regardless of visa issue date.
Entering the country on 60-day visa gives you a 60-day "period of stay" starting on the day of entry.
Catch here is if you want to do 90-day report online. If a hotel filed a TM-30 and you don't refile back at home, then you won't be able to do your next 90-day online
I'm guessing something in the package (maybe the eye drops) is being classified as a special product needing a license to import. Expensive lessons--we'vr had a few of those.
As far as the destruction fee. I've never heard of a logistics company being able to hold you on the hook for anything other than the import tax (if you choose to accept the package), as you have no contract with them. I'm guessing that's a scare tactic.
Either way, I would contact UPS central office and talk more with them.
They clarified the rules a couple years ago and said you don't legally have to refile a TM30 when returning to your regular residence. The only thing might be you can't file 90 day report online (they'll update the TM30 when you report at the immigration office). Should be no fine.
My understanding from a few officers I spoke with: it is not legally required to submit a new TM-30 when returning to your normal residence after travel in Thailand.
However, if a hotel submitted a new TM-30 while you were traveling, you won't be able to do a 90-day check-in ONLINE until your first TM-30 back is filed (can be at immigration, in that case).
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