It leaves Rodney Eade to step in as interim director of football operations while list manager Derek Hine will assist Eade with contracts.
Walsh hinted Thomas would soon put pen to paper and re-sign with the Pies.
"I don’t expect there’s going to be any issue there," Walsh said.
"I don’t think this is going to be drawn out because I know Dale wants to re-contract with the club, and certainly the club wants to re-contract ‘Thommo’."
Walsh said his departure wouldn’t delay the 26-year-old from re-signing.
"Paul Connors, Dale’s manager, has been away for a couple of weeks on holidays and he’s now back," he said.
"Before this situation (leaving Collingwood) arose I spoke to Paul last week and messaged him and said we’d catch up to resume discussions."
Walsh said he would be in regular communication with the football department during a three month ‘notice period’.
"I won’t be involved in the negotiations, that won’t be appropriate," he said.
"Other than (that) I have an agreement in place with the footy club that I will be available for the next period of time for anyone who needs some sort of advice or direction in terms of departmental issues.
"Certainly the salary cap and contracting position will be something I’ll talk to Derek Hine at his behest and the club’s behest."
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