From Command and Conquer Wiki

A chrono vortex is an unfortunate side effect of the use of Chronosphere technology and was one of the reasons the technology was recalled and abandoned. It is essentially a moving rift in the space-time continuum that would rampage through the battlefield, destroying everything in it's path. It appears as a giant whirpool of bending time, defying laws of physics.

The only way to counter a chrono vortex it to either run or send large amounts of units (amount depends on unit strength) into the vortex, distabelizing it and finally breaking it down. For commanders it could often be beneficial to sacrifice lots of infantry to destabelize it, rather than having to rebuild a base or a tank division, as it was cheaper to train infantry and send them into the vortex rather than loosing the former, wich would often mean certain defeat.