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Here's my workflow scenario:

 

1. Vendor uploads multiple county parcels into FTP server  - file is submited by county

 

2. Running on a scheduled task, FME unpacks and downloads each county parcel 

 

3. Each zip file is unpacked and stored in a shared folder with county sub folders. 

 

4. New feature classes are added in either in SDE or FGDB

 

5. Feature classes are added to an existing MXD using a layer file template

 

6. MXD is saved as MSD (perhaps overwrite an existing one)

 

7. MSD is then updated into ArcGIS server as a web mapping service

 

 

County parcels are in FGDB and SHP. Only the FCs in the FGDB will be merged into a single store for all county FCs delivered.

 

New deliverables are received weekly and updated quarterly. 

 

I'm thinking of using Python in FME for the functionalities that will translate the MXD, MSD, and layer files.

 

 

This involves almost 160 county parcels and 4M records that's why it would be good to automate this workflow.
It seems you have made a good plan. I havent worked with MXD and MSD-files, so not sure if there are any limitations there.
Do you need to do any attribute/geometry validation on the files?
Validation not required. Schme is expected to be the same across each deliverable.

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