They hammered Frank Lampard's Blues 3-0 in February's first leg in London, making Bayern among the favourites to be European champions. Bayern could face a disadvantage against potential opponents in the Final 8 tournament in Lisbon, due to start on August 12, from leagues which are not scheduled to finish until late July. La Liga runs until July 19, while the Premier League is set to end a week later, with Serie A not slated to come to a conclusion until August 2.
Only PSG and Lyon will have had less game time than Bayern and RB Leipzig, as Ligue 1 was ended early due to the coronavirus pandemic.
"We just have to make sure that we make the best of the situation," Flick said.
"It could be an advantage because one or two players would be available again."
Bayern's forwards are in stellar form.
Thomas Mueller produced a Bundesliga record 21 assists this season, while striker Robert Lewandowski has netted 49 times in 42 games, including 11 in the Champions League.
Bayern have been European champions five times and two of their 2001 title-winning team members are being groomed to take charge.
Former midfielder Hasan Salihamidzic is sporting director, while ex-goalkeeper Oliver Kahn will replace Karl-Heinz Rummenigge as chairman in 2022.
"In 2001, we won the Champions League together playing in jerseys, now we want to repeat that success with him in suits," said Salihamidzic.
"Oliver feels the same way -- we'll give everything to see it happen.
"It's our turn again."