Gephi files are known to be unstable in rare cases. Multiple workspaces might increase unstability. The team of developers is working at developing the next version of Gephi to solve these issues (see https://gephi.org/2013/rebuilding-gephi ... 9-version/
). In the meantime, we can just recommend to also save your projects in a graph file format, such as gexf - which is a solid and stable format.