If you are not careful to specify that the receiver do no HDMI video processing, then it certainly will modify the bitstream coming from the player. Exactly what it might do depends on the AVR's capabilities -- upscaling or framerate conversion for DVDs, for example. Often the scaler in a player (or display device) is better than what's in the AVR. Another issue is the signal level provided by the HDMI drivers in the AVR. If it's too low coming out from the AVR, it'll have problems driving a display over long cables. Also, it is my understanding that the HDMI outputs of some players have problems when they detect an AVR's HDMI repeater.
In addition, some gamers report that the delay introduced by an AVR's HDMI repeater can be noticeable.
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped