Just make sure the LLBLGen Pro Designer's Project Property CleanUpVsNetProjects is set to false.
This way your file won't be deleted when re-generating.
CleanUpVsNetProjects When set to true, the VS.NET project file task performer will first remove all file references for files from an existing VS.NET project file, before adding the files generated. For VS.NET 2005 projects, it will remove all files generated by LLBLGen Pro, as these are marked with a Generator tag.