As this guide uses a console command, it may well disable achievements for your playthrough. Hopefully Paradox fixes this bug on their end soon.
Those of you who use mods that modify the checksum need not care, as you won't have achievements active anyway.

First, make a flag file using this guide:

https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=2849886298

Follow the guide's instructions, but change the third line under colors={ to "null" in step 6.
Don't change any other lines.

The bottom should look like this:

colors={
"primary_color"
"secondary_color"
"null"
"null"
}
}

( You'll have actual color names for the top 2 lines under colors={ )


Other than that, follow the guide as normal, except do not have Diplomacy open when you apply the flag or you will be changing some other player's colors instead of yours.

You can also do this to the AI players' territories if you like, by having the relevant diplomacy open when you apply flag colors.

You may need to save and reload to get the full effects; I've noticed the inner space usually gets filled in with the primary color when you apply it, but on future loads it is the correct color.

BIG Thanks to TheDongsmasher for his guide!! That's how I learned to change flags in game using the console command.

Also, a thanks goes to the writer of the Flag Modding page at the Stellaris Wiki where it showed two nulls at the bottom instead of black above null. That's how I figured out what the bug was.

https://stellaris.paradoxwikis.com/Flag_modding

A final note:
This is actually my first guide on Steam!
So please let me know if I messed up somewhere and I'll see about fixing it.