Scribe 2 of 𝓟 initially wrote can not, then crossed out the not. His can not is probably a simple scribal error on his part. Evidence elsewhere argues that here in Alma 9:12 scribe 2 was probably not editing out a double negative from the text. First of all, multiple negatives involving “in no wise” do not occur elsewhere in the original text (or in the current text, as we would expect):
Spelling evidence also supports interpreting the initial can not in Alma 9:12 as a scribal error. Here scribe 2 of 𝓟 wrote cannot as two words, can not; yet everywhere else he consistently wrote cannot as one word (22 times). This regularity suggests that scribe 2 saw only can in 𝓞 and added the not on his own (thus the exceptional space between the can and the not, unique for him).
Finally, scribe 2 never corrected any of the actual double negatives in the text when he copied from 𝓞 into 𝓟. There are four examples, and in each instance the 1830 edition is also a firsthand copy of 𝓞. In all four cases, both 𝓟 and the 1830 edition have the double negatives, which means that 𝓞 did as well:
These four instances of multiple negation were removed only later, when the text was edited for the 1837 edition. Thus there would have been no motivation on scribe 2’s part to have edited out a double negative such as “ye cannot in no wise inherit the kingdom of God”. Double negatives such as these were possibly a part of scribe 2’s own speech, which may explain why he left actual examples in the text and here in Alma 9:12 initially wrote “ye can not in no wise inherit the kingdom of God”. The critical text will therefore accept scribe 2’s decision to delete the not that he had initially written in Alma 9:12.
The spelling of cannot provides other interesting information about the history of the text. Scribe 3 of 𝓞 consistently spelled cannot as two words (but there are only two examples), while Oliver Cowdery usually spelled it as one word (there are three places in 𝓞 and five in 𝓟 where he wrote can not). As far as the printed editions are concerned, only the later RLDS editions have used the two-word spelling. The spelling is mixed in the 1892 RLDS edition, with the two-word spelling consistently up through 2 Nephi 29:9 but then only the one-word spelling from 2 Nephi 31:1 on. The 1908 RLDS edition used the 1892 edition as copytext and has only the two-word spelling, probably because the 1908 compositor, having already set the first part of the text with can not, did not want to use a variant spelling for the rest of the text. Consequently, the current RLDS text has only the archaic two-word spelling, can not.
Summary: Accept in Alma 9:12 scribe 2’s decision to remove the extra not that he initially wrote in 𝓟 after can; usage elsewhere in the text as well as his scribal practice supports the correction to “ye can in no wise inherit the kingdom of God”.