I am having this same issue right now.  I was behind on entering bills so I just wrote a check and put it to a "clearing account".  Same as you, the original check is now cleared and here is what I did. 

• Be sure to take note of the exact amount and date it was paid.
• Enter the bills as you would normally
• Go into pay bills and pay bills and choose "assign check number"  Yes, this will create a duplicate check number.
• Then to into your check register.  (I sort by amount)  You will see both the original check and the check with the proper bills linked to it.
• Make a check mark in your register to clear the new check.
• Delete the original check from the register.

Even though you have reconciled, you are replacing the exact amount of the check with one that is linked with the bills and it has cleared, so it will not effect your reconciled bank account at all.

I hope this helps.  I have been doing this all day trying to play catch up :-)