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.
I did it twice adding new downloaded bootstrap, but always ends with same result. And importing of files switched to sync when the sum of the sizes of the blk* files reach ~2GB( bootstrap.dat.old have 2.37)
Yesterday I download newest bootstrap 2,38 GB (2 565 076 446 ) after adding in clam directory and launch client, importing blocks lasted few minute, than again switched to sync, although I am still in 26th January.
blk0001- 1,95 GB (2 097 155 946 bytes
blk0002- 195 MB (204 685 437 bytes)
bootstrap.dat.old - 2,38 GB (2 565 076 446 )