Man, I thought you would have done with ThemeHax. Let's troubleshoot:
1.Copy all 3DS folder to your PC.
2. Inside 3DS folder on the root of SD and delete all files and folders
3. Copy themehax_installer in this Themehax 1.3.zip into the 3DS folder on the SD
https://gbatemp.net/threads/release-homemenuhax.398124/page-23#post-5717329
4. Go to Home Menu Settings (the House icon on top left of the bottom screen) -> Change Theme -> Wait for the data to be created -> Exit back to Home Menu. Right now, it's not supporting custom themes (at least for common users) so better leave/restore it default.
5. Launch HBL using BrowserHax and install ThemeHax