Within the last couple years (is this the 2nd or 3rd), when trading has been allowed between the Rookie and Free Agent drafts, the rule has been that (players + picks) must be equal so that at the end of the FA draft everyone has 35 players.

I made trades last year that involved picks for players. For example:

MLESS Trade:Lafayette Leopards trades with Detroit Stars

3/18/2005 9:56:13 PM
Damaso Marte moves from the Detroit Stars to the Lafayette Leopards Active Roster
The Lafayette Leopards Round 1 Free Agent pick moves from the Lafayette Leopards to the Detroit Stars.

In practice, the rule that trades must include an equal number of FA picks applies from the time picks are awarded (game 65) until the cut to 27, thereby ensuring that each team will have 35 players at the end of the FA draft.

Yes, this does disagree with the manual. If you search the manual you will find several cases where things are currently done differently than what is listed in the manual. Things have changed and evolved but the manual hasn't always been kept up to date.