Editing a film with audio recorded at 44khz, 48khz and 96khz

As a rule of thumb, it is always best to have video audio (or audio for video) at 48kHz, not 44.1kHz. In my mind, YouTube simply should not allow 44.1k audio at all, as all international standards for audio in video are at 48kHz. The sole exception is on Blu-ray which does properly support 96k audio. DVD-Video allows 96k audio, but in general - and especially with motion video - this is overkill as unless the player is properly set to use 96k it will inevitably get downsampled on the fly which can cause artefacts to be introduced. You can easily run out of both space & bitrate too if using 96k for DVD, as the maximum bitrate for any stream in DVD is 10.08mbps, and for video & audio combined it is 9.8Mbps (or 9800 kbps) and 96k stereo uses almost 5000 of this, leaving very little for your video.

The 44.1k family (which includes 88.2 & 176.4k sample rates) is for CD, DVD-Audio & SACD only.

Upsampling 44.1 to 48 is painless as you are only padding with zeroes, but going down from 96 to 48 can be a little more problematic as there are unfortunately too many SRC (Sample Rate Converters) that simply lose every other sample and thus lose quality too. I highly recommend Voxengo's R8Brain (which is freeware) or their more professional R8Brain Pro.

Dropping from 48 to 44.1 requires whole number conversion, which most converters simply do not do and doing this should always be avoided.

Good question. I've had different editors and audio people tell me differently. From "I always use what I'm given and it almost always works fine" to 'I always resample to X" ... with that X being 44.1 for typical studio audio people to 48 for typical film type people.

The stereo/mono thing can be a pain for sure.

Neil