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>Added complications involve lots of QC testing and needing to know stock at locations, there is one physical warehouse but many quarantine and approved materials areas etc...

check out the KanBan model. Designed for precisely that kind of monitoring.
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>I think that once on the premises each material delivered can be given a unique batch or lot number that stays with it during it's lifecycle as you mentioned which will give traceability.

are they sufficiently important to their suppliers to be able to insist on the unique id for each incoming component? Thats by far the easiest...

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>My thinking is not fully formed as yet and it has gaping wholes in it! But I am modeling it out and working through it...!
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good luck