Pewande:
I lead a team of three business systems analysts, and we experienced the same problem of SharePoint Visios losing their stencils after a SharePoint upgrade.
Not sure about your situation, but ours was caused by a change in the SharePoint URLs that came with the upgrade. So when we opened a file or template in the upgraded environment, Visio was looking for the stencil using the old URL and could not find it. We solved the problem by opening the file/template from SharePoint, manually opening the stencil on SharePoint, then re-saving the file/template back to SharePoint. The result is that the Visio workspace is rebuilt with the proper stencil location using the new URLs. Next time we opened the file/template, Visio knew where to look. Problem solved.
We’re currently using Visio 2013 and SharePoint 2010, but I’m guessing the problem we had could happen with any version.
Hope this helps,
- Ken