Layer shift after pausing here too, I think it might be skipping steps when cutting filament as has been suggested.
Workaround that worked for me;
Instead of using adding a pause in Bambu Studio, add this custom g-code;
M400 U1 ;pause
G28 X ;home XY
That way, the printer does a XY home after changing the filament, and continues in the right spot.
(Shouldn’t this just be the default behaviour after a pause anyway?)