All I can think of is that they had to hustle the synd tapes off the NBC lot and get them to a dub house where they could be duplicated and bicycled around to the stations, so they had to pay for storage somewhere. The synd tapes, unlike the NBC tapes, didn't have to be stored at NBC between the tape date and the network air date, during which time an NBC A.D. would time them and NBC Broadcast Standards would listen for dirty words that had to be blooped. Then they would air on NBC and maybe HQ didn't feel it necessary to pay to store them. At that time, cable was in its infancy and no one thought these shows would ever be rerun in any venue. This was even reflected in the talent releases which didn't cover cable.
When HS left NBC for good, the lot was all abuzz because NBC wanted way too much money for the HS set which HQ wanted to buy from them. HQ said "screw you" and had a new set built from scratch. Apparently that was cheaper than what NBC was asking for the old set.
NBC was desperate for money in those days. At one point in 1979 or 1980 the fee packages went from 6 fee plugs at 7 seconds each to 7 fee plugs at 6 seconds each, and the announcers had to read 7 seconds of copy in 6 seconds. On Mindreaders I remember Ira Skutch checking with Johnny Olson to make sure he was OK with this, which of course he was. NBC was stooping over to pick up pennies off the floor.
Goodson always kept copies of all of his shows. He wasn't a visionary who could possibly have foreseen cable TV or any rerun value for his shows. Maybe he took a cue from Desi Arnaz and kept them anyway.