VCF format should not allow you to have different reference genomes. You should retain your 30 different files if they use different references.
Running the VEP is simply a case of running a command on the command line. If you want to run it 30 times and you don't feel like writing our the command over and over, you can just use your favourite scripting language to write a short script that runs through your list and plugs the appropriate values into the standard VEP command.
Edit: added highlighting to the text to make it clear what the OP needs to to next.