The approved BOM Version that gets copied to your Production order can be further maintained for just that production order. If you catch the production order in a created state, you can delete the Bom lines you don't need. The same is true of your route. It should also be maintained on the production order if it has costs associated with it that you do not actually realize in the repair process, or create a repair routing that you copy to these orders.
If you are past created (estimated, scheduled, started, etc) you can zero the quantity on the BOM line. You will need to re-estimate and re-scheduled the production order. But this will allow you to report as finished with out consuming items B,C,D,E in scenario 1. I am assuming this is where you will end up, as a repair operator might not know what they did until after the production order is dropped to the floor / started. You could alternatively 0 qty pick and end mark the picking list journal for items BCDE.
Note that this will cause cost variances if you are standard cost. You might want to consider having the parent item be a product master with a dimension to signify "reworked" or "New". Then you can have distinct standard cost price records for new vs. repaired units.