One of the first things the installer did was say "we notice you have an old version of Steam installed, we're going to get rid of it first then install the new version" so yes, all files in your old Steam folder are gone including HL2 media files. Unless you had them backed up somewhere. Sorry.
As to when the new media will be available, I think the last official word is still from the "Steam beta ending soon" announcement a couple of weeks ago, which said new media will be available "almost immediately" after the Steam 1.0 release. Whatever that means, hopefully today rather than sometime after this weekend.
well, the new steam client doesnt include a media section anyway, so you couldnt use steam to watch them anyway. But Valve just wasted a tremendous amount of bandwidth by making everyone re-dl several 100MB movies. It was lame to have only 2 options:
1. Waste like 3 gigs and have 2 steam directories or;
2. Erase everything and force me to re-dl a gig of shit.
There really should have been some kinda option to merge the installations.