I think you are confusing things... Analogue outputs from DVD player to amp mean you are getting all digital to analogue (D/A) conversion in the DVD player, so the amp is just amplifying the sound, and nothing more.
This means it doesn't matter what the digital sampling rate of the music was, because it has been converted by the time the amplifier sees it.
As for the digital path between DVD player and amplifier:
At this time only i.Link (firewire-based connectors) and a few proprietary options let you transfer SACD and DVD-A digitally between player and amplifier for conversion in the amplifier, and very few devices have this technology. A standard digital input on an AV amplifier (which is either coaxial cable with a tulip plug or an optical toslink connector) is designed for receiving sound off DVDs or CDs, which can be any of the following:
- PCM (2 channel 44.1KHz 16-bit) -> this is standard CD format
- Dolby Digital (up to 6.1 channels compressed)
- DTS (up to 6.1 channels compressed)
- PCM (2 channel 96 KHz 24-bit) -> only on DVD-videos
The last option is the one your amplifier manual is referring to. It gives manufacturers the option of providing higher resolution sound in 2 channel only format along with DVD videos. Very few manufacturers use this, since it is basically a lesser version of DVD-A and not supported by very many amplifiers for D/A conversion. Chesky records has made some recordings in this format, which actually sound very nice if you have an amp or DVD player capable of converting them well.
Note for your information: DVD-A has two options: 5.1 channel 96 KHz 24-bit, or 2 channel 192 KHz 24-bit...
So final conclusion: That option you changed will only effect the replay of a few recordings via digital out from DVD player to amplifier. DVD-A recordings have to be transferred via analogue cables, as do SACDs, and your kit should be fully capable of replaying them fine.