Just for the record - Had the identical issue in a fictional league (162 game season).
Checked my 'upcoming free agents' page at years end and resigned the couple players I wanted to keep. FA signing time started and Bam....4 extra players gone, including my entire starting outfield......sigh.
Won't negotiate w/me either.
I wrote it off as a 'broken' game issue and began laboriously doublechecking every darn player, every year end......and began signing extensions to all players I wanted to keep once they had 5 years service time in. Seems the Arb Eligible tag keeps them from being listed as possible FA's....even tho they are.
Only 4 years in this League tho, so still testing, would be very interested in hearing conflicting/supporting further evideence that I'm on the right track.
Regardless.....'feels' broken anyway....
