Upgrading ISV Layer - AX 2012 R2 to R3

Dears,

We are upgrading our Dynamics AX 2012 R2 to R3, we have customization on the ISV Layer, the ISV supplier does provide an upgraded model of the ISV (R3) but it has many changes from the R2 version, some tables are deleted and functionalities have been changed.

These changes can effect our system as we are using some of the deleted objects in integrations with third party software and we have many customizations on top of these deleted objects.

Is it okay to move all the ISV customizations to a clean VAR Layer and upgrade it? will that cause any issues for the future? or is there a better way to achieve that? 

Thanks a lot.

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