What are the contents of the microSD card in the R4?
Original firmware can be downloaded here from the wayback machine:
https://web.archive.org/web/20201125165450/http://www.r4isdhc.com/2014-r4isdhc-gold-pro/
Direct link (in English):
https://web.archive.org/web/20201125165450/http://www.r4isdhc.com/KerneDownload/R4i-V4.0b English.zip
To check if it is still installed, place the flashcard in the 3DS. Use a magnet to find the spot near the A/B/X/Y buttons that puts your 3DS in sleep mode. Make a note of that.
Power off the 3DS, place a magnet in the spot to sleep the 3DS, and then hold Start, Select, X, and Power for about 5 seconds and release it. If NTRBoot Flasher boots instead of the 3DS home screen, it is still flashed for NTRBoot.
If it is still setup to use to install NTRBoot, use this to remove it. Specifically the "Removing ntrboot" section:
https://3ds.hacks.guide/installing-boot9strap-(ntrboot)