You don't really provide nearly enough information for a decent analysis, for instance the application, base motor speed, installation, motor failure description etc., but here are some generalities.
The problem with running a motor over base frequency is that the motor output torque is going to decrease at a logarithmic rate proportional to the overspeed, and if the load torque requirement is higher than that output torque, you are overloading the motor. For example if this was a centrifugal pump, the load power requirement will increase with flow, which increases with speed. So even if your motor was oversized by 20% at full speed, a 50% overspeed will have increased your power requirement by 50%, but your motor power remained fixed, meaning the motor was 30% overloaded (very rough math, but you can follow the idea). Most VFD's motor protection algorithms are sophisticated enough to provide protection in this circumstance, but I cannot attest to the 1336's ability, you would have to ask A-B.
You are correct to worry about the bearings, but to be honest most 20HP motors use common parts, so an 1800rpm motor uses the same bearings as a 3600rpm motor, so that may be irrelevant. If you have a 3600rpm motor that you were running at 5400rpm however, you may have in fact cooked the bearings. You need to check that out with the motor mfgr.
Harmonics are an issue regardless of overspeeding, so if your motor design was not meant for VFD operation, it would only be worse running overspeed. Severe Duty does not specifically mean suitability to VFD operation. In particular, did you consider the distance from the drive to the motor? There are many issues regarding that, and if you ignored them, the fact that it was overspeed was not necessarily the culprit.
Also, some motor cooling fan designs lose effectiveness above base speed, so that may contribute to premature failure. Again, check with the motor mfgr.
Those are but a few of the issues at hand. Have a motor shop analyze the mode of failure in the motor. Sometimes that can give you a way of narrowing down the possibilities.
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