12:55:12 Stage: Build
12:55:13 Server To Agent Workspace Sync
12:55:13 Started syncing files from the server ‘localhost’ to the agent ‘myagentpc’
12:55:16 Finished syncing files from the server ‘localhost’ to the agent ‘myagentpc’.
12:55:16 MyApp
12:55:16 [Fatal] The working directory “C:\Continua\CI_WS\Ws\20908\1MyApp\Buildsys” does not exist.
I can reproduce the error, but the path you are using is invalid. The correct way to refer to the workspace is $Workspace$. I am surprised that $Source$ ever worked. Which version did you upgrade from?
$Source.MyRepo$ refers to the folder that the source files are copied to. In your case: C:\Continua\CI_WS\Ws\20908\MyApp. This only works if repository rules for MyRepo copy the files to a single folder.
$Workspace$ refers to the root workspace folder. In your case: C:\Continua\CI_WS\Ws\20908. This can be used more generally for files outside of the repository paths.
I will look into changing the error message to state that $Source$ is invalid if used as such in an expression.