Pl advise: fertility treatment + flare??

hi
We have been planning to start a family for more than an year now, our last gyn/RE has suggested clomiphene citrate challenge test... i am worried to take any medication or have any test on body fearing it might result in a flare up. Last time my RE suggested some vaccination before we start a family and that vaccination gave me a flare up... i am now worried about any more experiments with my body :-( ... the treatment was left midway because we shifted from arizona...now planing to see another RE here. I guess to help us conceive they might give me some strong medication.

Has anyone gone through any kind of fertility treatment and had a flare up? are there any medicines i must avoid? pls let me know so that i am prepared incase my new RE/gyn suggests any new test/medication .

thanks!