hairy_hen said:
... Playing the AC3 file with ProLogic 2 seems to discard the bass channel for some reason, but DTS Neo:6 retains it, thankfully, although the placement of elements is probably different. ...

Prologic II generates its own LFE/.1 channel by upmixing the Lt/Rt channels to 5.1, so this is to be expected.

I've no idea how my system would handle a 2.1 file, probably just play through the front left and front right speakers with the LFE sent to the sub-woofer - so the centre and surround channels would be lost.

Would be interesting to create a plain Dolby Prologic 4.0 upmix from the 93' audio, then add your LFE channel to the mix and encode as 4.1 AC3.