I found a solution, not sure if it's the best one, but it's working. Figured out how to initialize a new cookiejar, copied the good cookie into that. Opened the bad page (corrupting the cookiejar) and replaced the corrupted cookiejar with the clean one.
Code:
import copy
goodcookies = br._ua_handlers['_cookies'].cookiejar
clean_cj = mechanize.CookieJar()
cookies_to_copy = []
for cookie in goodcookies:
copied_cookie = copy.deepcopy(cookie)
cookies_to_copy.append(copied_cookie)
for copied_cookie in cookies_to_copy:
clean_cj.set_cookie(copied_cookie)
# request that corrupts the cookiejar
br.open(q_init_search)
br.set_cookiejar(clean_cj)