Enterprise Plus doesn't track rentals for credit, so it doesn't matter if your rentals have your e-Plus number in them. All e-Plus does is make the rental transaction a minute faster, as the agent doesn't have to type all your driver's license information in each time.

If you have a National Emerald Club account, however, you can earn Emerald Club Rental Credits with your Enterprise rentals. I don't know if you can modify your existing Enterprise rentals with your National EC account, but the Enterprise rental agent should be able to add it at time of rental.

As for crediting past rentals to an Emerald Club account: don't know and haven't heard anyone's experience from here. Kinda interested to see if it's possible, though...