It's true that a company can't issue ISOs if the termination window is more than 90 days, they have to be NSOs instead. IMO the downside of the NSOs (pay tax immediately upon exercise instead of at next year's tax deadline - ISOs don't actually change the amount of tax that is due, just the timing of when you pay it) is small compared to the very real risk that your options will go poof if you don't have the cash to exercise and pay tax if there is a termination event.
No, by law ISOs just convert to NSOs at 90 days. Startups themselves decided to expire them, there is nothing preventing them simply allowing them to change. You get worse tax treatment, of course, but at least you get to retain the ability to participate in the upside.
