I lived and worked legally in Taiwan from 1997 to 2006. In that time, for various reasons I never took out permanant residence. Now for various other reasons, I’m considering a move back. As I understood it, you could apply after 7 years of living in Taiwan. Should I return, would those previous nine years count, or would I have to start all over again? Thanks for your help in advance.
I do not know about PR, but for an Article 51 work permit (the so-called “open” paragraph 3 for non-married foreigners) you can still qualify within 2 years of your last departure from Taiwan.
Make sure you make your first application a good one. I was denied a third Article 51 on the basis that by that time, my 5 continuous years had not ended within the last 2 years. I don’t know how PR works but I’d hate to see you get rejected for some stupid reason (missing document, or something) and then go back a little while later and have them say, “Now you’re not qualified anymore.”
Hopefully someone else will have better information, but you’re right to ask and to be VERY aware of precisely how many days have passed since you left Taiwan - and don’t forget this is a leap year!! 
Under Article 23 of Taiwan’s Immigration Act, you can apply for permanent residency within two years after completing the required residency period. (I suggest you make all possible haste, because it takes a while to get all the certificates and documents together – see many related threads on this board.) Good luck!