You can add the pin number back by using Add > Text as follows: (Symbol Editor - .dra)
1) Add > Text
2) Under the Options tab change to Class Package Geometry and Subclass to Pin_Number
3) Select the Pin that requires a pin number assignment
4) Select location for the Pin number text and enter the pin number
If you have a lot of pins that need the pin number added back in it may be easier to re-add the pins again.
If you accidentally deleted the text on Package Geometry / Pin_Number in the layout (.brd) the pin will still remember its pin number. If you want to get them back graphically just refresh the symbol using Place > Update Symbols..
Hope this helps,