A little trap that comes with the "Hughes" legacy of these parts.
It is possible that input shaft and the whole TRGB for that matter can be fitted to either a 269
OR 369.
The life limit is LOWER on the 269 most probably due to the uneven power pulses of the piston engine.
In days of old you could swap these items between models as long as the lowest life was taken into consideration. This practice is now prohibited by TCDS.
If this shaft has history of being fitted to a 269 it may be the issue. Life on a 269C of a 369A5425-5 is only ~ 8600 hours yet on a 369 it is "on condition."
I would look closely at the previous "history" of this shaft.
As for the tooth dropping off, it is not the first and probably not the last one!
We are talking 50 year old design here.