Even I am getting the same error.
Thanks in advance
In general, it is not a great idea to just delete folders within your Server install. They could contain actively used extracts or workbooks.
That being said, as extracts are refreshed, the old extracts are deleted eventually after all the sessions connecting to that one have been closed. Check your Background Tasks maintanence views and look for Reap Extracts to see if that process has been suceeding. If it has been failing, it is likely that old extracts are not being deleted.
Regardless, Matthew has the right idea: loop in our support team. Addressing this issue via the forums would be difficult.