@ts > First of all, please update your players to the latest firmware, 4.10 - available here: http://www.pioneer.eu/eur/support/software/CDJ-2000/index.html
Did you make note of which track this happened with? Can you replicate the issue with the same audio file?
You were using one CDJ as the host and had the second CDJ linked (i.e. all running from the same USB stick)?
If you are playing music from CDJ-A when the USB stick is connected to CDJ-B, then power cycling the unit will cause everything to stop playing.
As for vinyl brake, were you in Vinyl Mode and had the brake settings adjusted accordingly?