Tutzu,
Answering your questions
1) No, we also allow connections which do not have representations in the config file.
2) Unfortunately, there was a bug in 3.8.4 which resulted in user connections (like the one you created) not being persisted and restored correctly. This has been fixed in ME 4.0m1.
Having said that, you should have only lost your user connection(s), but there should have been no exception caused parsing the .mex file.
Delete the .mex file (this stores layout and connection information) and try again.
Do you get an exception if you stick to just creating standard forward and input connections (connections which have representation within the struts config file?)
Since user connections are not persisted in 3.8.4, I would suggest not using them entirely until you move to ME 4.0.
Sorry for the inconvenience, this was a bad oversight.
Let me know if anything is unclear or you need further assistance.
Brian.