Don’t know if you’re still trying to figure this out, but I struggled with the same issue until finally getting things to work. Here’s how to do it:
- Open up a new Blender window and start by Saving a .blend file right off the bat (doesn’t matter where):
File > Save > my-new-startup.blend
- Now instead of Appending the brushes Link them:
File > Link > [navigate to your brushes and select them for linking]
- Now go into Sculpt Mode and select one of your new brushes. You’ll see this button:
Note that the preview thumbnails for these brushes may not appear. Don’t worry about that for now.
- Click it. Do the same for each of your new brushes (it’s a pain, I know).
- Almost done. Now we make all paths to external data absolute:
File > External Data > Make all paths absolute
- Save your .blend file again
File > Save
- Finally, you can save the Startup File:
File > Save Startup File
All done! You should now be able to close Blender and your new brushes will be present each time you open a new session. The preview thumbnails for each brush should also appear upon re-opening Blender.
At first it may appear that there are duplicate brushes when you’re selecting a brush in sculpt mode. This is not the case; Blender just has a terrible brush selection UI.
As a side note, you can delete the “my-new-startup.blend” we created during step 1.
Also, it’s worth noting that with this method you can save the source files for your custom brushes anywhere you like; you don’t necessarily have to save them in “C:\Users[USERNAME]\AppData\Roaming\Blender Foundation\Blender\2.79\config”. If you, for example, have a folder where you keep all of your custom Blender assets you can stick them here.
Either way, another benefit to this method is if you upgrade to a new version of Blender and migrate your startup file, your brushes should still be present. This is due to us making all paths to external data absolute. I have tested this by upgrading from 2.79 to 2.8 and haven’t noticed any issues thus far.
Honestly this whole process is way more difficult than it needs to be, and I suspect it may have something to do with v2.79. Either way I hope this helps you and whoever stumbles across this post during their travels. Good luck and happy sculpting.