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I created a Sharepoint search center with the refiner "file type". All document types related to the keyword are shown in the filter except Visio files (vsdx), but if I edit the search page and preview the refinement configuration it shows all file types:

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How can I include all file types in the search filter sidebar?

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For 2010. From Why are some Refiner values hidden in SharePoint Search and FAST?:

But a very common question comes up around Refiners, with regard to deep and shallow behavior. I'm sure you know the definition well: FAST Search for SharePoint has deep refiners, which means that each result in the result set is processed and used when calculating the refiners. However, SharePoint Search uses shallow refiners, where the refiner values are calculated from the first 50 results only.

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If you cannot see a specific value on the Refiner Panel, that means:

  • In case of FAST Search for SharePoint (deep refiner): No result matches this refiner value at all.
  • In case of SharePoint Search (shallow refiner): No result matches this refiner in the first 50 results.

For 2013. From Refiners in SharePoint 2013 Search:

we do have deep refiners in SharePoint 2013

So the next thing to check is the "Maximum number of refined values" setting in your refiner webpart.

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