Is it possible to create a workspace that automatically updates the schema table (attribute table) every time it runs?

I created a workspace that takes a zip file (nested zip), unzips it to a temporary folder (I used StartUp Python Script to do so). It then reads all the unzipped SHP files from the temporary folder (uses dynamic ESRI Shapefile Reader), reprojects all the files, filters them by feature type (to points, lines, polygons), checks for duplicate features and if the geometry is valid. Finally, it saves 3 output shapefiles:

1. all point elements consolidate into one output shapefile

2. all linear elements consolidate to one output shapefile 

3. all polygon elements consolidate into one output shapefile

I would like the workspace to be independent of the input dataset (attributes). Because now when I run workspace with a second set of zipped shapefiles (with different attributes), I get shapefiles in the output with empty attributes that are in the first set of data. 

For example first dataset (which was used to create workspace) has ‘A’, ‘B’, ‘C’ attributes, second dataset has ‘D’, ‘E’, ‘F’, ‘G’ attributes. After running workspace with the 2nd dataset as an output result I got a consolidated  shapefiles with null (missing) ‘A’, ‘B’, ‘C’ attributes. And I would like to get consolidated shapefiles with ‘D’, ‘E’, ‘F’, ‘G’ attributes as an output result.

I would appreciate any tips.