Question does my 90 days start again with this new number or will it be linked to old one?
Cant give you a definitive answer - however, the data stored is not just held under passport number. Just like the UK, when your passport is scanned (or read via the chip) all of the data is read and stored, name, DoB, place of birth etc etc. How sophisticated their (TR) data matching process is I don't know, but it certainly has a capability to pick up on new passport numbers when all prior data is the same, or similar.
I know we've discussed dual nationalities using both their passports to circumvent the 90/180 rule, but in your case other than passport number and validity dates I suspect the vast majority of data will be similar. I suppose what I'm saying is that there is the likelihood that they'll match it up, but given the issues they have with the system, maybe they wont. Not a lot of help really!
JF