I don't have the FTDNA nightmare you have but I just discovered an issue with Ysearch whereby when I entered or uploaded the 67 markers tested with FTDNA, three untested markers were converted to 0 when you click on save while others not tested were left with a hyphen.This happens whether manually entered or you use the automatic upload on your FTDNA page.I asked another researcher in my surname project to check their upload to Ysearch and they found the same result.I notified FTDNA through their Helpdesk after trying to reload the DNA info using both manual and automatic methods with the same result.Their reply on November 16, 2013 was:
"Thank you for your email.This looks to be a bug in Ysearch since every time I set the value for the marker to - (not tested) it resets back to 0.You may try deleting the profile and then doing the automatic transfer but I cannot guarantee that this will correct the problem.The IT department is aware of this issue but I do not yet have a time frame as to when it may be corrected.I apologize for the inconvenience this causes."
I decided to send another note asking whether the Ysearch program is therefore compromised and might result in mismatches.Reply of November 17, 2013:
"Thank you for your reply.The answer is it might, in certain situations.Since the User ID has three markers entered as zero these markers would be taken into account but only if you select running on a comparison to users that tested at least 70 of the same markers.If it is anything below that it should not make a difference."
As far as I know, they have not notified people who have tested with FTDNA about the Ysearch bug. I think people should know and be aware of the possibility of mismatches.In fact, I would advise everyone to check their data on Ysearch to see if 0's were entered for markers not tested.They should remain hyphens.
If anyone else encounters this problem, I advise they also send a note to the FTDNA Helpdesk.That might get the "bug" fixed sooner.