The Supreme Court ruled on Friday that subpoenas could not be issued to biochemist Charter and compound pharmacist Alavi to compel them to give evidence.
Former Australian anti-doping boss Richard Ings said that made it a "one-all scoreline" between ASADA and the players, with the penalty shootout to come.
Ings noted that while ASADA had a big win in the Federal Court three months ago when it ruled that the joint ASADA and AFL investigation into Essendon's contentious supplements program was legal, Friday's Supreme Court verdict was undoubtedly a setback.
ASADA was still set to present statements from Charter and Alavi at the tribunal hearing.
But the Herald Sun revealed on Monday that Charter had met with Essendon and one of the players' lawyers to discuss potential weaknesses in ASADA's case.
Charter reportedly met with lawyer Tony Hargreaves, who acts for 32 of the players charged, and Essendon chief executive Xavier Campbell on November 7, and had a further telephone conversation with the pair last week.
The two-hour November 7 meeting was recorded and transcribed into a 50-page document that could form part of the players' defence.
Charter said he was "neither ASADA's witness nor Essendon's" and denied he had been paid to stop cooperating with ASADA.
"Tony Hargreaves has had the opportunity to discuss some issues that were unclear and also to clarify the chronology of the peptides ordered," Charter said.
"There were a number of flaws in ASADA's case and it was going to be hard for him to fill in the gaps if I wasn't turning up."
The tribunal, to be held behind closed doors at the County Court in Melbourne, will rule whether the players are guilty of taking the banned substance Thymosin beta-4.
If found guilty, the players risk bans of up to two years.
