Telerik Document Processing is part of several Telerik bundles and could be upgraded following the steps for upgrading the other assemblies from the suite with which you've obtained the product.
Starting from Q1 2016, the Document Processing assemblies have an assembly version which may differ from the assembly version of the other assemblies in the particular suite.
Starting from R3 2016, only assemblies with a version number ending with .40 suffix are distributed. The libraries don't contain code specific for .NET Framework 4.5, thus an additional version is not needed.
The changes are synced between the controls that have a dependency on Telerik Document Processing and while the referenced files are from the same release, they should work as expected regardless of the version distinction.
Due to the specifics of Telerik Document Processing, a project that uses only assemblies of this product cannot be upgraded using the Upgrade Wizard of Visual Studio Extensions. You can manually replace the assemblies with the new ones or change the project's references to point to the location of the new version.