I think, you can go ahead and activate the datasource from RSA5 transaction, collect it in a transport. It should not effect your existing appended fields,
we got a similar problem for other datasource, however it is not that delta capability is given as part of upgrade, but the datasource has got ODP concept and we followed the instructions in the below SAP note, 1764182
it may be applicable to your case also, you can give a try in Sandbox, see that your appended fields are exist after activation.