I have been using VeraAlerts to push alerts from Vera to Pushover, and use the Pushover app for those alerts on my 2 iPhones for quite a number of years with no issues. According to my license, I purchased VeraAlerts on 2/10/17.
If you changed Veras, your license is tied to that controller. I switched from a Vera 3 to a Vera Plus last fall. Rather than ask Richard to move my license, I just purchased another license for the new controller. This also allows my Vera 3 to be a backup controller.
If Pushover is working, I suspect something is not working with VeraAlerts. VeraAlerts should not care what the Pushover specific target devices are.