AbstractHandler#getOutputFileToWrite(Obs) is the method that provides the File instance to write to when saving a complex data file to disk.
It constructs the target file name to be used based on the obs 'title':
And if the outputfile already exists, then it works on a new file whose name is made unique with a two-digit suffix.
This works only up to the 100th file:
The 100th file will just be blindly overwritten.
Overall the design of this method should be challenged, down to the way it retrieves the extension out of the filename (why not use Apache's FilenameUtils?)
I suggest a complete rewriting that ensures that the provided File instance is properly named and safe to write to.