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This was a long-standing bug since Luma3DS v8.0. If you changed the homebrew title and didn't immediately reboot, then the ExHeader during termination would not match the ExHeader that was was used for loading the process, and thus sysmodule process refcounts would get all messed up. The obvious solution to this is to ensure no application is running while changing the hbldr titleID (hence the changes in custom PM). This was quite possibly one of the cause of homebrew failing to load when using N3DS H&S.
3DS Loader Replacement
This is an open source implementation of 3DS loader system module--with
additional features. The current aim of the project is to provide a nice
entry point for patching 3DS modules.
Roadmap
Right now, this can serve as an open-source replacement for the built in loader.
There is additional support for patching any executable after it's loaded but
before it starts. For example, you can patch menu to skip region checks and
have region free game launching directly from the home menu. There is also
support for SDMC reading (not found in original loader implementation) which
means that patches can be loaded from the SD card. Ultimately, there would be
a patch system that supports easy loading of patches from the SD card.
Build
You need a working 3DS build environment with a fairly recent copy of devkitARM, ctrulib, and makerom. If you see any errors in the build process, it's likely that you're using an older version.
Currently, there is no support for FIRM building, so you need to do some steps manually. First, you have to add padding to make sure the NCCH is of the right size to drop in as a replacement. A hacky way is this patch which adds junk data. Play around with the size value to get the NCCH to be the exact same size as the one found in your decrypted FIRM dump.
Once you have a NCCH of the right size, just replace it in your decrypted FIRM and find a way to launch it (for example with ReiNAND).