When re-running a ABAQUS job getting the old files existing message. Is it possible to over-ride it without having to type Y?

This could also be a problem if ABAQUS is run in an optimisation loop many times automatically. 
This can be done by adding the following line to the abaqus_v6.env in the directory from which ABAQUS is run (for example).

ask_delete=NO

If running ABAQUS on a PC then make this change to the system copy which will be in the ABAQUS installation directory : 
C:\ABAQUS\6.8-1\site\abaqus_v6.env 
This needs to be used with care. Accidentally typing the name of a previously carried out analysis (which may have been a long run) which you didn't want to be deleted/overwritten can easily be lost with the above setting (as there is no safety net). 
When not required change the setting / or comment it out / or delete it.

# comment it out
#
# ask_delete=NO

# Reset it

ask_delete=YES