Somerset opener Trescothick returned home Wednesday after a recurrence of his stress-related illness forced him to quit the Australian tour, and was replaced by Middlesex batsman Ed Joyce.
Trescothick's dramatic u-turn is considered a blow to England's chances.
But Botham is still backing England to retain the Ashes Down Under, and he expects Flintoff to tell his players to "get stuck in and fill their boots".
"Flintoff will be disappointed, but not disheartened, by the reshuffle" Botham told the Daily Mirror.
"I know he will regard it as a major opportunity for those left on the tour to take the fight to the Aussies.
"He will tell them to forget about what has happened in the first week, to get stuck in and fill their boots.
"One thing he will not tolerate is any pessimism. I get so cheesed off when people respond to setbacks with doom and gloom - especially in Australia, who will trample all over you if you show any sign of taking a backward step.
"He'll tell them to face the front of the class and face facts: England hold the Ashes, and if they think positive the Aussies will have to play out of their skins to retrieve them."
Joyce will join the Ashes squad in Adelaide Friday, where England is playing a three-day game against South Australia ahead of the Nov 23 opening Ashes Test in Brisbane.
Trescothick suffered a stress disorder that forced him to take a complete break to recover during England's India tour last February and the subsequent English summer.
Trescothick, who will be 31 next month, has played 76 Tests for England, scoring 5,825 runs at 43.79 with 14 centuries.