I addressed this in your previous post on the subject. Custom materials are not saved when saving as a tool (.ztl, via Tool> Save As). Only the material “slot” is saved, with whatever material occupies that slot by default.
So, for instance, if you saved the tool with the Red Wax material applied but made changes to that material, the .Ztl. will load with the original Red Wax applied but not with any changes you made to it.
In order to re-apply those changes to a .ztl, you would have to save the modified material out of the Material palette as a .zmt, then load that .zmt in the same menu into the red wax material slot on your freshly loaded .ztl. The custom .zmt will then overwrite that slot with with your changes anywhere that original red wax was applied.
Saving your file as a .zpr, via the File> Save As menu will save custom materials with no further action required, but is a less economical file format than a .ztl, saving lots of other information as well. So generally, one might work on the tool’s geometry early on via the .ztl format, or in a situation where that additional data isn’t required, then switch over to a project file when setting up a scene or a render. The reason you would care about file economy is because the larger a file gets the more potential performance concerns come with it, depending on system.