I have a Samsung la40a650a1fxxy 40in lcd TV and I've lost sound through the tv's speakers but if I turn on the amp for me surrond sound it comes through is there a reset sequence I can go through any ideas appreciated

Yes,
You surely will find a "restore factory setting's" option in your menu

Just see around, and you will find it.

Before resetting your settings entirely, go into the sound settings and look for "Speaker Select" Or something along those lines and make sure "External Speaker" is not selected, but instead you want to select "TV Speakers".

Also, if this does not work, how did you have the amplifier connected? Did you run it off the audio output off the TV?