Emilie,
Since all changes are processed in TM in one way depending on process controller settings and the user ID is always the remote user, I think some part of this logic has to be written on ERP side.
When a sales order is saved you could check if a user has manually changed date or quantity and then set some flag on the TRS0 message. You may have to use a BAdI for the relevant interface to be able to add a field on TRS0. If you require this indicator to be on the FU, then I suggest you use a custom method to read the OTR and update the indicator on the FU.
Best Regards,
KC