Problem of... friction!
Basically the problem can be summarized in this word: 'friction'.
When printing a flexible TPU filament such as Filaflex in an 'All-Metal' hotend such as the Prusa MK3S printer, something very common that usually happens in this type of hotends is that it does not have a good internal polished surface or may suffer from poor cooling in the barrel area.
Therefore, during printing, we are likely to experience intermittent or discontinuous filament flow problems.
Thermal expansion
And you may ask, what exactly causes this discontinuous or intermittent flow, why does it print so badly?
This problem is caused by the thermal expansion that the filament undergoes inside the barrel and by its high predisposition to grip it to the barrel surface. This effect will increase as the filament becomes more elastic. That is, if we print with filaments with lower Shores, for example, Filaflex 70A or Filaflex 60A, the grip will be much greater and the impossibility of printing, too.
The elastic filament tends to stick to the internal, hot, metallic surface of the barrel, making it very difficult to flow and print correctly. It will produce jams and discontinuous material extrusion flows.