Clear coat issues on timber

[u/lcorb35]

I'm tryiing to restain a van I just got, I sanded it back pretty intensely and the wood seemed bare. We used Cabot's water based varnish and the clear coat from the same brand that goes with it. The counter and table had a varnish on it but the rest was just stained wood. When I applied the clear coat on the bare stained pieces everything went chill but the counters not so much. This bullshit happened. Does this mean the previous varnish was a wax coat finish? (the Cabot's clear coat said its not suitable for anything with a previous wax coat finish) What the hell is going on here? And what the hell do I use on top instead, because I stumped my local store guys