We are using an automated design tool to edit SolidWorks assemblies that have been converted to STEP. The process looks like this:

1. Convert parts from SLDASM to STEP.

2. Assemble parts in automated tool.

3. Save Assemblies from tool as STEP files.

4. Convert Assemblies back to SLDASM from STEP.

5. Insert Converted Assemblies into template 2D Drawings. 

These template drawings are pre-dimensioned  to the original models that were sent into the tool as STEP files, however, when the modified files are brought back in via a reference replacement in SolidWorks Explorer, all dimensional references on the 2D drawing are lost (They turn yellow and are unable to reestablished). We also lose all BOM data from the parts, which was to be expected. 

Is there anyway to remedy this using STEP files, upgrading to STEP 242 or using SW 3D interconnect? Or is just an issue inherent to STEP files?