This is still an issue. I imported a .gexf file, applied some partitions, duplicated the workspace a couple times and applied a single attribute equality filter to each workspace. I have done this with different data sets. One attempt resulted in the error message described in previous posts. Most attempts load without error; however, workspaces are missing and all filters are applied to a single workspace and converted to the one that was applied to that workspace. Furthermore, there is an issue with the way the data is loaded as applying the filter results in all nodes filtered out. Note that the filters were boolean fields.
Hopefully this helps narrow the scope a bit. I also recommend the issue be a high priority. It is very annoying--to say the least--to start from scratch every time you want to analyze a data set (though it did improve my Gephi skills...).