Can i apply the topical estrogen if i am still of reproductive age? my urethra prolapse occured due to straining during a urinary infection.

Yes, but: Estrogen cream doesn't help prolapse ot helps urethral caruncles which usually only occur in post menopausal women and aren't prolapse.

Yes: Typically, you don't get enough systemic absorption to disrupt normal menstrual cycles. Applying it to the urethra sold be no problem. If you are currently predictable in cycles, you probably are getting enough estrogen and the topical cream might help some but wont be something you have to do for long.