The subordinate conjunction that appears to be necessary here, although it was omitted in the 1837 edition and not restored until the 1879 LDS edition and the 1908 RLDS edition. The tendency to omit the that after the very same clause (“and then shall it come to pass”) is found in the following verse:
In this second instance, Oliver Cowdery initially wrote the in 𝓞; but then he immediately corrected the the to that by overwriting the e with an a and writing the final t inline. Here in Alma 40:12–13, the critical text will, of course, retain both instances of “and then shall it come to pass that S” (where S stands for a finite clause).
Summary: Maintain in Alma 40:12–13 the subordinate conjunction that after “come to pass” in this future-tense expression with inverted modal (“and then shall it come to pass that …”).