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If you rename a protocol using F2, then this only renames the actual collaboration of the protocol. The other internal elements, i.e. the <<ProtocolContainer>> Package and the three <<RTMessageSet>> Interfaces does not get renamed according to the naming rules for the internal elements of a protocol. Steps to reproduce: 1) Create a UML-RT model 2) Create a protocol in this model 3) Press F2 to bring up the dialog to rename the element 4) Give the protocol a new name 5) Save the model 6) Open the .uml-file directly in the UML model editor 7) Observe how the <<ProtocolContainer>> Package and the three <<RTMessageSet>> Interfaces still have their old names, and only the <<Protocol>> Collaboration have gotten the new name. It must be ensured that the internal elements of a protocol gets renamed correctly, disregarding in which way the protocol is renamed, e.g. using F2, using the properties view. This is guess also highly related to the functionality to be able to edit the name "inline" in the model editor, which will also be possible to trigger using the F2 and replace the modal dialog that pops up. See Bug 492356.
The fix for blocking bug 506895 is available in the latest Papyrus Neon.2 nightly builds.
I have verified this in the latest Papyrus-RT build. All the internal elements of the protocol (<<ProtocolContainer>> Package, <<Protocol>> Collaboration and the three <<RTMessageSet>> Interfaces) gets renamed according to their naming rules when using F2.
Closing as verified fixed.