You make all your blueprints as part of a module in the toolset with your new/updated haks. Save often.
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Once you have all your blueprints made, keep the module open in the toolset. Open your NWN/modules/temp0 folder. It contains all of the module resource files for the currently open module.
If you sort the list by file type, you can find all of the .utp files...these are the blueprints for placeables. Copy all of the files you want to another folder, then close your module.
Open your hak with the new palette file(s) in it, then put all those blueprint (.utp) files in the hak and save it.
Now, any module you add that hak to in the toolset will (after you do a "build") should have both the new palette(s) and the blueprints you made in your original module.
Just keep in mind that while you can open hak-stored blueprints in the toolset via the "edit" option when you right-click on them, the changes won't be saved to the versions in the hak...and the game will use the hak version rather than the updated version in the module itself.