Can thermal....energy change by means other than heat( let's say when
mechanical work is done on the system)
If by "thermal energy" you are referring to internal energy, then yes internal energy can change by means other than heat. It can change by the same amount by doing an equal amount of work, since the change in internal energy is related to heat and work by the first law:
where $Q$ is is positive if heat transfers to the system and $W$ is positive if work is done by the system.
For example, in the case of an ideal gas where internal energy depends only on temperature, you can increase the temperature of the gas with heat with no work, or by doing work (compressing the gas) with no heat (compressing it adiabatically). The end result is the same increase in temperature and the same increase in internal energy.
But then when you pull the brakes in your car, the tires, the road
everything becomes hotter aka they gain thermal energy.
In the case of disc brakes, when you step on the brakes the main things that get hot (experience a substantial increase in temperature) are the brake pads (which are stationary) and the rotors (which are attached to and rotate with the wheels) due to kinetic friction between them.
In effect, the majority of the loss of macroscopic kinetic energy of the vehicle (kinetic energy of the vehicle as a whole when it decelerates) is converted to microscopic kinetic energy (an increase in the molecular kinetic energy of the brake materials which results in an increase in temperature), and thus the internal kinetic energy of the brake materials.
The actual slowing down of the vehicle during braking is the result of the counter-clockwise torque that the brakes apply to the wheels. The force of that torque acting forward on the ground is opposed by the equal and opposite static friction force that the ground exerts backwards on the vehicle per Newton's third law. This backwards force, neglecting air resistance, is the only external force acting backwards on the vehicle and is thus responsible for decelerating the vehicle.
Now (ignoring rolling resistance), there are no frictional losses at the contact surfaces between the ground and the tire as long as the maximum possible static friction force is not exceeded so that the vehicle skids on the ground. So as long as the vehicle doesn't skid, the only transfer of energy in the form of heat to the ground would be in the form of heat conduction from the brake materials to the ground.
Eventually, the elevated temperatures of the brake materials relative to their environment (other materials in the vehicle and its environment including the ground) will result in energy transfer in the form of heat to the environment.
Hope this helps.