Any changes made to a Contract after it is generated will then show as "YES" in the Modified After Generated column when in the Generate Contracts task. 

The only changes that will take place are the Tuition & Fee amounts (this includes Deposit), and any other data will stay the same. This sentence is what states the change:

User-added image

Other changes will not update (ex. Payment Plans, Not Returning, etc). Currently we do not have a way to see what the change was within the contract generation screen after the change is made. 

The Contract Generation Review report, does not show a Yes/No for generated contracts but will show what the current tuition, deposit, and fees are.

If you have Contracts showing "Yes" for Modified, then you re-generate the Contract, those contracts will no longer show as "Yes" for Modified unless a change is made after the Contract is generated again. It only indicates if changes were made since the last time the Contract was generated.