Hey @susie.campbell,
Unfortunately the Tiller Community Solutions Add-on version of the split and reconcile workflows are not designed to work well with reconciling already-split transactions. (Transaction matching for reconciliation is a lot more complicated when the transactions are split into component parts. 
)
With the current tools, I would recommend splitting transactions after they are reconciled.
As for the specific transaction causing you headaches now, I’d just reconcile that manually. Just delete the manually-entered one and port any relevant details into the feeds transaction (this is essentially all the reconcile workflow does).
Going forward, we are thinking on what a production manual-transaction/reconciliation workflow could look like if it were within the Tiller Money Feeds add-on. I’ll suggest to product-manager @heather that we consider making these two tools play better together.
Cheers,
Randy