@Ken_GlassWire I am experiencing this issue again and this time I know the cause!
I updated the firmware on my system drive SSD, after which all apps are re-prompting and duplicate firewall rules are being created. To be clear, the physical drive, logical drive letter, program path and file hash are unchanged. But I guess some underlying drive ID has changed. This makes me think that perhaps the same thing could happen if something like the storage controller driver was updated. I am running v2.2.268.
Here is an example of a duplicate rule:
{GlassWire.in.app_-1379453621.profile_1.mode_2} GlassWire All Yes Allow No c:\program files (x86)\razer\razer services\razer central\razer central.exe
{GlassWire.in.app_1956058586.profile_1.mode_2} GlassWire All Yes Allow No c:\program files (x86)\razer\razer services\razer central\razer central.exe