We were in the midst of reading the Torah on Shabbos when a siren went off. We all ran to the bomb shelter. What is the proper procedure from there and onward when we return.
After the threat has passed, the congregation is to return to the Shul and continue with the Torah reading from the area where one left off. This applies even if the Olah, or Baal Korei, spoke in the interim, and applies irrelevant of how much time has passed. No before blessing needs to be repeated unless the interval occurred after the Olah completed his first blessing prior to the Baal Korei beginning his reading, in which case the Olah must repeat both the Barchu and the first blessing, upon his return.
Sources: See Michaber 140:2; Ledavid Emes 6:61; Birchas Habayis 44:26; M”B 140:6; Ketzos Hashulchan 25:8; Kaf Hachaim 140:11; Yabia Omer 1:9; Piskeiy Teshuvos 140:2