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Unfortunately, there is no option to store extended properties outside of the database being documented. I have a logged feature request with reference SDOC-1437 and will be informed if/when the status of this changes.
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Here's how i'm planning on doing my documentation (i'm just now starting this):
Create my initial documentation on a version of the databaase either on my local machine or on dev
Copy the extended properties to dev/test
Any additional documentation will be made on the dev server and then copied up from there (done right before a version push to test)
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We don't make changes to our production system except through our standard dev/test/staging process, so I can't just point SQL Doc to our production system.
Thanks!