Mine did the same thing, manual transmission, thought I lost the clutch, pulled the engine and found the transmission input shaft has slid back into the transmission. I can pull it forward and it engages with splines in the transmission, but there is nothing to keep it from sliding right back into the trans. Right now I am trying to figure out how to split the trans and the differential. There must be some sort of keeper that let loose.

could also (more likely) be related to "inching" (far left pedal 'clutches" the transmission, if the actuator cable is binding, the valve spool in the transmission will not release the spool enough to allow the transmission to engage properly).