There error message in this case says exactly what the problem is. I'm guessing that you used something like fastx tools, that can't handle paired-end reads, to quality and adapter trim your reads. If you use trimmomatic, trim_galore, or something similar then this won't happen.
Anyway, the simplest way to resync the files is to use repair.sh that comes with BBMap. You can see Brian Bushnell give an example of that here.