If the app shows up in the Apps tab and there is an option to remove it, then do that. Otherwise you should only have to upload all the files in the zip file. They will overwrite the older existing plugin files. If you have created any devices using the old plugin I’d suggest you delete them.
Unzip the ZIP file to a location on your PC
Open your browser to the VeraPlus page - connecting to your Vera
Select the Apps tab on the right
In that tab select Develop Apps
On that page select Luup files - that will list all of the files on your Vera controller
Select the Upload button - that will open a dialog allowing you to browse to where you unzipped the zip file
Select all of the files from the zip file
Select the Open button in that dialog
Once the files are all uploaded the Vera will restart. When that is complete (all the lights on the Vera are back on) go back to the Develop Apps page on the Vera and select Serial Port Configuration. In the Used By Device drop-down you should be able to select the RFXtrx device. Make sure it shows baud 38400, data bits 8, parity none and stop bits 1.