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When managing versions in ArcMap with layers from different geodatabases, the version manager dialog displays only one particular geodatabase regardless of which layer or datasource is highlighted in the Table of Contents (TOC).
This is a known issue.
The ArcMap version manager determines the version to be managed from the properties of the topmost layer in the table of content. Highlighting in the TOC a different layer from another geodatabase and clicking the Version Manager tool on the versioning toolbar does not manage that geodatabase's versions.
Use one of the following workarounds: