RE: Incorrect Journal Entry Link to Sub Ledger?
Can not say that I have seen this one specific in the recent months, but it can happen - not sure why, but I have heard of it and there are a few things you can try to resolve the situation.
First, if at all possible take a backup of the LIVE database and create a TEST company so that you can work with the data in an environment that will not effect production. Since we are not talking about changing any code or writing any kind of utility at this time, you can do this on the same SQL Server and GP Code base as you use for LIVE access. If we progress to a point where 'code and scripts' might be employeed, you might at that point consider a TEST SQL Server installation and a separate TEST GP Code installation.
Having taken care of the 'CYA'
I would suggest in the TEST database that you run a full check links on the Finance and Payables modules to see if anything shakes free.
Secondly I would be sure to run reconciles on the Financial Year and Batches to again see if that forces anything.
Post results when you know if these were effective.