The problem is not that you can't add it to an existing booking, it's that you almost certainly can't add it to a booking made through a third party (in this case Expedia).

That has always been the case AFAIK with most rental car companies and in fact also most hotel program companies. If you book through a third party, you often can't earn anything else on the booking, so you can't add your own frequent travel number to the rental car booking.

That also applies to "vacation packages" which include a rental car; in those cases you also can't add your own frequent travel number to the rental car booking.

Meanwhile, when you say new rates are $250 more now, a couple things to keep in mind:

1. Are you just looking at rates with no discount, or are you trying various airline discounts at Hertz? (Sorry, I'm not sure which airlines have the best discounts at Hertz now, I used to always book Hertz through United Cars -- providing my Hertz Gold number at United -- but United just dropped their partnership with Hertz a few months ago.)

2. "Pay later" rates often drop significantly at many locations but if so only a week or two out from the reservation date, typically not earlier.