To summarize, and a solution:
16:18:56: !ERROR!System:Rigid meshes not supported! Asset: ears.gr2, Mesh: ears
16:18:56: !ERROR!System:Rigid meshes not supported! Asset: hairbase_mop.gr2, Mesh: hairbase_mop
This is because you are still using the default characters and not your own dynamic character. The .gr2 extention is no longer supported for dynamic characters, but are still there on the default ones. Bennett can fix this, but probably won't, since you would want your own dynamic character in place before release (this is a must actually).
16:18:56: SYSTEM:System:Room Default wants to load EnviroScheme Area but area Clean Test has none (a default scheme will be created)
You are travelling to the clean test area. Log in to a different area by travelling there. Don't delete the clean test area if you don't know what you are doing. You can easily setup a different area for a "safe-harbor" if anything goes wrong through code.
16:21:33: SYSTEM:System:ActivateAreaSpec 9223372056919021606 assigning ID 9223372056919021606 instance 5
Shows me you are travelling to a play instance; if you remove the tree in a play instance, the edit will not b e persistant. You would want to remove it in the edit instance [Instance 0]
16:21:33: !ERROR!System:SpeedTree \speedtrees\broadleaf_rt\broadleaf_rt.srt state 0 has detail_texcoords but no detail map; ignoring coords
This can be ignored. This is an output by the engine, but gives no penalty to performance. They are working on "fixing" this, by probably just surpressing the error.
16:21:37: !ERROR!System:Connection to Server Lost: Connection to Repository Lost
Well, damn

16:21:37: !ERROR!System:GUIGhostInterface::Build(RFIF): GOM ERROR: GOM::addNodeFromPrototype (10554): error: with InternalException message 'Unable to create an instance from the prototype(1000000298), as it is not a valid prototype id.' node=1000000297
Did you remove any user interfaces, or did you edit anything that you have not told us? Though as this is after the connection lost, the blade wants to load something from the repo, but since it cannot connect, it cannot build. So probably nothing wrong there, and I can conclude you did nothing with the user interface as of yet.
16:21:37: !ERROR!System:GUIGhostInterface::Build: Failed to create GUI control. name=GUIPanel
See aforementioned.
Solutions:
Try and delete the tree from the repository browser. The engine will hopefully give just an error message like "Error loading file (File not found)". Hopefully, the blade will not crash... and you can remove all instances in the edit instance with the Assets menu.
For the rest of the errors, they are related to this, so try this first and report back

Don't worry about the rigid mesh