I cannot imagine how misalignment causes reverse precession unless the misalignment causes a rub.
It is not really physical reverse precession.
The math transform provided transforms two vectors (x and y magnitude/phase at a given frequency) into two other vectors (forward and reverse magnitude/phase at a given frequency).
If we have pure circular motion (x magnitude matches y magnitude) in the forward direction (x leading y if rotating CCW), that gives a pure positive frequency vector.
If we have pure circular motion (x magnitude matches y magnitude) in the reverse direction (y leading x if rotating CCW), that gives a pure negative frequency vector.
Any other combination of x and y vectors which is not purely circular (equal magnitude) can not transform into pure positive or pure negative and therefore must transform into a combination of positive and negative frequencies.
If we have pure linear motion (phase of x matches phase of y), then we get equal magnitude positive and negative frequency components. This particular case is well familiar to those dealing with electrical motors - the linearly oscillating field of a single phase motor can be analysed in terms of a sum of equal forward and reverse rotating fields. Also the simplest (textbook) 3-phase motor has three linearly oscillaing fields (one per winding). Each of these three fields has a forward and reverse component. The spatial and time arrangement of the three windings is such that the reverse components of the three phases cancel and the forward add giving pure rotating field.
Misalignment creates a preload which MIGHT create something resembling a linear orbit with equal positive and negative frequencies (also might create banana shaped with harmonics or other stuff). For that matter unequal H and V stiffness can cause non-circular orbit.
An interesting case where physical reverse precession does occur is when very unequal H and V stiffness give a "split critical" (different resonant frequency H and V direction). If we are far above the H critical but far below the V critical, then the 180 phase shift caused by increasing speed through the H critical causes reverse precession. The negative frequency will likely be higher than the positive frequency in this region.
Actually I don't think Don Bently was the very first person to conceive of this transformation applied to rotating equipment. I think W Foiles was the very first (sometimes posts here). There are a lot of others on this forum as well that work with this stuff a lot more than I do. Steve S, Steve C, Walt S. etc. Maybe some of those guys will chime in if I have said something wrong.
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