That doesn't make any sense flashing a boot.img shouldn't remove the mod haha. Weird. Anyway for future, simply flashing over the top of the other mod would be fine.
I did flash the mod over the other one the first time but I had both v4a installed then. Of course the 188.8.131.52 driver was installed but I was also switching kernels so I flashed the boot.img and it deleted the reboot app, dolby app and both viper4android apps.