Filing a separate state return as married filing separate

I filed a married filing joint return for the Federal and NYS personal tax returns.  The taxpayer works in CT, and it is less costly for the taxpayer if I file married filing separate in CT, which is allowed by CT.  I filed the Federal and NYS with no issues.  I then created an additional file using "save as" and with a slightly different name.  When I tried to file the CT in the second file, I received a message that there were errors in the federal return in this new file, and I would not be able to file the CT.  Obviously, I am not filing the Federal return, only the CT return.  In the previous year, ProSeries walked me through this and I don't recall having to correct the Federal return in order to file the separate state return.  I also don't recall the procedure they used.  I spoke to tech support and this person had no idea, and said someone could call back within 24 hours but that would be too late.  I will probably just file a CT extension from the original file to resolve this today.  But I still will need to resolve this.