This might be a bit of a beginners question but I was wondering if there was any benefit to working in Pro Tools at 96k 24bit when all your sounds will be bounced out and used at 44k 16bit ?
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In my opinion, working with 96KHz in a project intended for 48KHz is minimizing the risk of audible degradation while mixing several sources together, as well as when using effects. There are actually some programs that handle higher frequencies worse then lower ones, but that's very rare. What on the other hand is very important is that you use a really good converter when down-sampeling it, or everything you gain by using the higher setting will get lost, and perhaps then some...
Higher bitrates are practically always a win situation, but sample rates can be a little tricky if you're unsure about your monitoring. It's important to use your ears and pay close attention to what happens when you experiments.
Having a session in a higher bit rate will allow a larger dynamic range, allowing you to get away with more gain staging with less chance of clipping in your channel. Higher samples rates in your session allow you to time stretch your sounds while retaining more high end frequencies (as the ones that are in audible then roll down into the audible range). You should always work in 24 bit when possible. 96k isn't necessary usually unless doing some sound design. Regardless, it is standard now to work in 48k no matter what you're working on and it is very easy to down-convert. I always work in 24-48 and 96 when I edit sfx, do sound design, etc.
If you are going to end up with 44.1 kHz, 16 bit files, you are better off working at 88.2 kHz. Downsampling from that sample rate is simpler mathematically--you are cutting the sample rate exactly in half. Going from 96 kHz to 44.1 kHz is a lot more complicated--the best sample rate converters can do it pretty competently, but why take a chance on artifacts occurring when you don't have to?
For film, of course, you are aiming at a final product at 48 kHz, so then you would use 96 kHz (or 192 kHz) in your initial recording.
BTW, I think the main benefit of recording at higher sample rates occurs during the initial A to D conversion--real world problems with anti-aliasing filters are moved up at least an octave which makes the artifacts less audible. Recording at 24 bits is always desirable as well--any audio level processing that occurs during editing will be done more precisely, and you can leave more headroom during the initial recording. Only when you are rendering the final file should you dither down to 16 bits.