Ok, two things to say here.
1) how to handle model versions
The internal identifiers (GUIDs) for the objects in your DEV model are different from those in your PROD model, because you generated a new DEV model. If the GUIDs are the same, the Merge operation will link keys that have different names; without the GUIDs it will assume that Key_1 in DEV matches Key_1 in PROD.
Instead of generating a new DEV model every time, why not either:
- take a copy of the PROD model to be your DEV model, kept in a separate folder - do this via 'File | Save As' or just by copying the file in Windows
- this will have the same GUIDs, so objects match up OK
- a better option is to create DEV and PROD branches in the repository, consolidating DEV changes into PROD when you need to
- you can have multiple DEV branches if you need to, each with different permissions
2) how to match up two similar models with different GUIDs
When you generated the DEV model, did you keep the generation links from PROD to DEV? I think the merge operation can use these to match things up. If you didn't keep the links you can re-create them.
- In the PROD model, use Tools menu option to generate to DEV in update modde, setting option to keep generation links. In the merge dialogue, match any objects you need to match, deselect all actions (so it doesn't update any objects), then click <OK>. This should re-create the generation links.
By the way, when you're merging, don't forget that you can save the current selection for use again later.