It's very hard to re apply the Item ledger entries with the correct Lot if user wants to reapply the Stock with the correct lot no to get the correct cost related to that Lot. if it is partial qty case then there is no chance to correct from the Item application work sheet except to do the correction from the backend from the Item application entry.
Another case for the credit note time also it's not applying with the correct Lot, manually user needs to apply credit note stock entries with the Invoice Items stock entries.

Please let me know if you need any example/ further clarification related to this. Thanks for your support in advance.