Thanks for the info so far guys
I guess I was thinking those 45k people were going to eventually click the activation link in the email in the upcoming 6 years (j/k) until I recently emailed them all a new activation link and realized most of the emails bounced back.
I guess I should never let this happen again sounds like the best idea. lol
Pruning or deleting means I have to click 999 members one by one 45 times. That sounds like a really great option right there. Thank goodness for support forums or else I might of had to click 999 members one by one 45 times.
I am looking into a PHP fix as mentioned above.