signrawtransactionwithwallet seems to break the existing signatures of some of the inputs

まず、提供された署名前と署名後の raw transaction、および signrawtransactionwithwallet RPC を使って問題を再現し、その後、別の input に署名する際にすでに署名済みの input がどのように扱われるかを調査します。完了条件は、既存の有効な scriptSigs が変更されず、それらの input について RPC が無効なスタックサイズを報告しなくなることです。

It seems that this rpc alters the scriptSig of all of the inputs that were already signed (second and third vins in this case), except for the first one.
This is an example with 4 inputs, where the first 3 are transactions that are already signed:

Before executing signrawtransactionwithwallet, I have this transaction:

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

and after executing it, I get this one:

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

By decoding both, it seems that this RPC alters the scriptSig of all of the inputs that were already signed, except for the first one.

The error that is returned by the RPC on the inputs that were already signed (second and third vins in this case) is:
"Unable to sign input, invalid stack size (possibly missing key)"