I am missing nights as well. I had 24 SPG nights so far this year, I started the merge and it shows 13 "lifetime" nights. I bailed on the merge process at that point, and tried logging into spg.com with my "new" spg number and it shows 13 nights for 2018 so far. :|
Update, the missing stays that make up the 11 missing nights are now showing up in my (unmerged) spg account (using the new number), but it's still saying I only have 13 nights for 2018. Points seem to be correct.