How can we reconcile the Hadith, "Leave that which makes you doubt for that which does not make you doubt," with the command of the Prophet, peace and blessings be upon him, to perform Istikhara regarding matters that cause perplexity and doubt?

There is no contradiction between the Hadith about abstaining from doubtful matters and the Hadith about Istikhara (seeking guidance from Allah). The first calls for abandoning anything that involves doubt to ensure safety, while Istikhara is performed for permissible or recommended matters that a servant wishes to do. It is not performed for obligatory, recommended, forbidden, or disliked matters.