I spilled water on the RM-AAP040 that came with my STR-DN1000. The RM-AAP040 is dead, i took it apart and didn't see any water or damage but it doesn't work at all.

I purchased a RM-VL610 which works the receiver but it seems to change everything but the HDMI inputs.

Do I need to buy a replacement RM-AAP040.

Well, the problem is at minimum you'll need to find those codes somewhere to learn them from. You might want to invest in a cheap UEI-based remote to use as a donor (you'll probably find the VL610 better to use for daily functions). Or, you could see if you can find someplace with a compatible remote that would learn you learn the codes (ie. the place that sold you the receiver).

The HDMI inputs on the STR-DN1000 use Sony 20, device 16.40. The only UEI remotes which are known to be able to provide those signals are the RCA RCRP05B and the OneForAll URC-8820N. See www.remotecentral.com/cgi-bin/mboard/oem/thread.cgi. Others can't send sub device 40.  You will need to spend 5 minutes or so doing some manual programming.