You mean RESET the Scale Tool...
Nice, thank you. I'm well aware that its barely past 6 years but this is exactly what I needed.
No worries, we still consult 2000 thousand years old book for today's problems this helped a lot!
This not working with me in maya2019.
What I did is
Moved the manipulator to the bottom of the object in D.
The object was grid-snapped. (To allow the object to scale like 3dsmax.)
When I scale here, I get the error I mentioned earlier.
Just to be sure, pressing D and right-clicking in the orient mode of the manipulator, right-clicking on the Marking-menu, and selecting Reset Pivot and snapping the manipulator to the bottom of the object again did not change the situation.
The overall scale is fine, but it sucks.
the scale option
In the modelling toolkit, go to scale settings and choose object. I had it on world and i changed it to object and the warning disappeared.
This warning happens when you scale the object in object mode, but didn't use the object space for axis orientation (Scale Tool Settings > Axis Orientation set to Object). By default, Scale Tool use object space as pivot orientation, and any scaling you made is stored in object's transform node Scale.XYZ attribute and this attribute only uses object (local) space. When you set Axis Orientation other than Object, Maya has to save the scaling as tweaks directly into the shape node. You can see those tweaks in Channel Box's CVs (click to show) when you select the vertex. This is called "baked onto".