I don't understand what happened, but I would suggest stopping your client, renaming bootstrap.dat.old back to bootstrap.dat and starting the client again. It will re-read the bootstrap.dat file skipping the blocks it already has and importing the ones it doesn't have. That might work for you, but I'm not sure. I don't know why it didn't import all the blocks the first time through.
Could you show the size of your bootstrap.dat file and the size of any blk* files you have too?
For example, I have:
-rw------- 1 user user 2097152626 Oct 31 2017 blk0001.dat
-rw------- 1 user user 496629018 May 15 02:45 blk0002.dat
-rw-rw-r-- 1 user user 2565076446 May 12 03:46 bootstrap.dat
The sum of the sizes of the blk* files should be about the same as the size of the bootstrap.dat it imported from.