Why did you uninstall the CFW? If you have any problems, this is not a way to solve them. There is a nice sticky thread about this:
"You don't need to remove B9S" The guide to proper troubleshooting
By uninstalling you delete the tools that could help you solving any problems. It’s like leaving the house and shutting the door without taking the key with you.
Even worse is the possibility of bricking the device if system files have been modified.

Okay, that being said: Are you really sure you uninstalled B9S? Did you use the uninstall option of the GM9Megascript?

In general reinstalling the CFW is possible. Version 11.9 leaves you the options ntrboot with a compatible flashcart and Frogminer and hardmod if you’re very good at soldering.

For Frogminer either follow this guide:
https://jisagi.github.io/FrogminerGuide/
or the Frogminer path of Plailect’s guide:
https://3ds.hacks.guide/

Before trying Frogminer (again), make sure your DS-mode works (start any normal DS game or the DS version of Download Play if don’t have a DS cartridge at hand).

 

The CFW does not interfere with online features. And unless you do really stupid things like cheating online or playing leaked games before official release, there is almost no ban risk on the 3DS.

Please describe this a little more. What interface do you mean? Upload a photo if possible.

For the case the spam protection does not allow you (because you're a new member) to post a picture or a link to an imageboard send the link with some blanks:

https:// my-example-board. org/ picture. jpg

 

I think I got it now. You used Seedminer to install B9S in the past and the modified save with the exploit and the b9stool are still there (and hopefully all the other files) mentioned in the guide.

https://3ds.hacks.guide/installing-boot9strap-(seedminer)

First make sure the cfw is really uninstalled by holding "SELECT" while booting. Luma settings will pop up if it is still there; else it will boot normally. In case it is deleted you should be able to proceed normally with the guide (if all needed files are on the SD). But because I'm always unsure and paranoid, please @TurdPooCharger have a look at this.

 

Can you try another litmus test to verify you don't have custom firmware?

1. Download the *.7z Luma3DS v9.1 from here.
2. Extract the boot.firm and place it on the root of your SD card. Use 7-Zip.
3. Reinsert the card into the 3DS, turn the system on, and hold the (Select) button.

Do you see this?

​

 

The presence of custom firmware files and folders are not enough to go by in determining whether or not your 3DS system still has custom firmware installed.

The litmus tests suggested by KleinesSinchen and I are the sure proof ways in confirming whether you still have it or not. If you follow the Frogminer method and mistakenly try to install custom firmware with it already on, you can end up bricking the 3DS. Because removing custom firmware may leave behind orphaned files, the B9STool may misidentify your system still having custom firmware. You can override the warning but only if you're positively sure there is no CFW.

 

Okay, I think you're good to go continuing with rehacking the 3DS using Frogminer, but just to be extra safe, I'm going quote someone who knows this better.

 

Lol, because I suck with *miner(s) family of hax's, I'm call someone who know this better than anyone else. Calling THE Frogminer guy, @zoogie!

 

...even if my software version is supposedly uncompatible?

 

What part is incompatible?