Hi,
We have had a lot of experience with Adagio Inventory sites and also are Chartered Accountants. Years ago we insisted to most clients that they run with FIFO to ensure GAAP and struggled to deal with these same issues mentioned above.
Now we are older and wiser, and more practical. There are very few situations that really warrant FIFO where you need the lots for separate tracking of costs for accounting or real cost tracking purposes. It's more practical to convert your data to Weighted Average and eliminate most residual cost issues, and problems with loading count values, or adjustments to the wrong cost pools.
You should consider the quick fix to permanently collapse your cost pools to Weighted Average, and your problem goes away. You backup your data and change the cost method in your control account set.
There will be tons of feedback saying that this is just wrong for accounting but we live in a practical solutions world, and it just makes sense. And we've seen the numbers and the differences today in most businesses using Weighted Average instead of FIFO, are nominal.
But for those have have a defined requirement and your accountant insists on FIFO, you should stay with FIFO and dream about what if I could only make this way simpler.
Best,
Brian