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At minimum I'd review the manufacturer's installation instructions and warranty terms applicable to the specific shingle that was installed. It would seem normal that the warranty will be affected if instructions are violated. If you find that the installer or his supplier's delivery crew violated the instructions and jeopardized the warranty, you should ...
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The holes just above the missing part and the way the missing part is textured, looks like powder post beetles.
Look for the same entry holes on other rafters. It seems on that one piece the entry holes are only on a certain color of wood, perhaps sapwood, not the heartwood.
You may be able to sister another new piece beside the damaged one, but do not do ...
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looks like a CLB (continuous lateral braces) and probably should NOT have been cut down!!
https://www.finehomebuilding.com/2007/11/06/why-brace-some-truss-webs-but-not-all
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