I'm using a Swiss emergency passport valid until 13 September 2016. I already extended my 30 days visa-exempt entry for THB 1,900 until 13 September 2016 showing them my Thai ID card. I'm planning to go to Hong Kong and Macau in about 2-3 months and apply for a re-entry permit. In Hong Kong and Macau they allow 1 month passport validity. Can I still re-enter Thailand with a Swiss emergency passport with less than 6 months validity but with a re-entry permit inside? According to Timatic with a Swiss emergency passport need 6 months passport validity but I think if less than 6 months with a re-entry permit is also acceptable.

Then I plan to apply for a new Swiss passport at the Swiss embassy in Bangkok in August or September and depart from Thailand to Cambodia or Malaysia on a cheap flight on the last day when my old Swiss passport is valid (13 September 2016) to re-enter Thailand a few days later on my new Swiss passport. Should there be any problem when I plan to depart Thailand on my last day when my old passport is valid as I can enter Cambodia or Malaysia on my new Swiss passport?

Would it also be possible to use a cheap visa run company from Bangkok to the Thai-Cambodian land border on 13 September 2016? But I guess there will be some complications as they probably don't allow to switch from old to new passports at land borders to Myanmar, Laos, Cambodia and Malaysia.

I suspect you will run into trouble with this plan at some point. Emergency travel documents are intended to allow urgent travel when you unexpectedly find yourself without a passport. The expectation is that you will promptly replace it with a regular passport.

That aside, I assume you have PR status in Thailand, and received the extension on the strength of that. If so, it would be up to the IO on arrival whether they would waive the six-month restriction on ETDs. I doubt this is a common scenario, and I think you are taking a hell of a risk.

If you have a Thai ID card and have gotten an extension as a returning Thai national why don't you get a Thai passport and use it for your next next entry to the country.

I also suggest you apply for a new Swiss passport instead of relying on the emergency passport.

I'm mixed Swiss and Thai born in Thailand and could also make a Thai passport. But for going to US/AU/NZ it's better with Swiss passport. Also I can make VAT refund. I have friends in US/AU. In case of Swiss emergency passport they issue a US visa in 2 days. With Thai passport I would need to wait around 2 weeks for a US visa. I don't mean I live in Thailand forever. It's only for about 9 months. Now I just moved to Thailand. After 9 months I will return to Switzerland and apply for a regular passport. But I think getting a second Swiss emergency passport in a row won't be a problem because as far as I know they don't issue regular passports in Swiss embassies if you still are registered living in Switzerland.

I'm mixed Swiss and Thai born in Thailand and could also make a Thai passport. But for going to US/AU/NZ it's better with Swiss passport. Also I can make VAT refund. I have friends in US/AU. In case of Swiss emergency passport they issue a US visa in 2 days. With Thai passport I would need to wait around 2 weeks for a US visa. I don't mean I live in Thailand forever. It's only for about 9 months. Now I just moved to Thailand. After 9 months I will return to Switzerland and apply for a regular passport. But I think getting a second Swiss emergency passport in a row won't be a problem because as far as I know they don't issue regular passports in Swiss embassies if you still are registered living in Switzerland.

You can use both passport for travel. Just use your Thai passport for entry and departure for Thailand. Use your Swiss passport for entry to other countries that don't allow the same entry if you use a Thai passport.

Lots of people use both their passport when traveling.

At the moment I don't have a Thai passport and Thai passport is really useless for me as I don't go to Russia and Mongolia where I would need to apply for a visa in advance with my Swiss passport and for Myanmar, Cambodia and Vietnam I don't mind to pay some money for e-visa or visa on arrival. And I can make VAT refund in Thailand with my Swiss passport.

OP

why not secure a new Swiss passport, have the visa stamp transferred to it (valid up to 13 Sep), get a re-entry permit, and be on your way. i suggest you iron out all your travel documents before leaving. you're sort of living on the edge using documents that are about to expire. i doubt if any user here takes the sort of risk you plan to take.