In ConnectWise, the ContactURL contains the version number. When 3CX adds contacts from ConnectWise to 3CX, it includes the version number available at the moment. When you upgrade your ConnectWise installation, new contacts will be created with the new version number, but old contacts with the old version number will remain. The only solution is clearing these contacts from the 3CX Console > Advanced > Contacts > Bulk Delete > CRM Contacts. This will remove all the contacts synchronized from ConnectWise, and start adding them again using the new version number.
Regarding the popup happening when the call rings, unfortunately this can't be customized at the moment. The only option you have would be setting the Web Client > Settings > Integration > Off, so no automatic popup is launched, and manually click the contact card just before answering the call, so you see the contact details.