If you reload the Web console and go back into that node, is the connector really gone?
Does your filter have any wild cards that another node might be matching the criteria?
If that doesn't explain it, go to the system in question and remove the tools. In Windows, look for C:\Windows\SysWOW64\ContegoSPOP\tools. Remove the XML files but leave readerState.xml! Restart the Agent Service and see if they come back.