As I understand the further upgrade can fail if we try to update the class which already has scheduled job in the managed package, right?
Attribution to: Natallia
Possible Suggestion/Solution #1
Yes, That is right. You can avoid it by writing your logic on other classes and just call it from the scheduler class.
How to deploy apex classes that are scheduled
In older version scheduled classes and all other classes which are refereed in scheduled class were used to be lock. With new version now only scheduled classes are locked. So if you move your logic in other classes it should fix your problem.
Attribution to: AtulRajguru9
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