The HFO DVD is weighted towards Henley and Walsh. Other songs were recorded but didn't make the cut including Peaceful Easy Feeling (Tempchin). It's an odd selection but doesn't really support Felder's allegation that it was to avoid paying royalities to Meisner and Leadon.
There's a strong correlation between the writer and the singer of an Eagles' song and so it doesn't seem surprising that a song gets dropped when the singer leaves rather than have someone else sing it. The exception is Take it to the Limit and each time Frey sings it, Meisner will be collecting royalties.
None of us know what went on when the Eagles were putting together Hell Freezes Over but it must have been a delicate process and it's hardly surprising that they didn't complicate things by trying to include all the former band members.