When you reload the palette in the toolset, this wipes the temporary toolset palette (which isn't a palcus.itp), and starting from scratch, grabs the pal.itp, detects all blueprints in your module, and sorts them into your toolset palettes based on the category number of each of those blueprints.
Making it So Custom Templates (Blueprints) Do Not Appear on the Palettes
Although not recommended, some Builders and CC makers find it convenient to directly modify the template files (e.g. UTC, UTI, UTP files, etc.) for vanilla resources, placing them into a HAK file attached to the module. Unfortunately, this method has the undesired affect of having the modified template appear on both the Standard and Custom Palettes. You can fix this by opening the template file with GFF Editor (available in the /util/win32 folder of your EE installation) and changing the PaletteID to 255. The modified template will still appear on the Standard Palette but not on the Custom Palette.
-written by Symphony in Discord