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Ok, I’m still not clear on exactly what you’re trying to achieve as I can’t quite see the connection between somehow preventing certain files being duplicated when cloning the disk and preventing yourself from reinstalling the system.
Bear in mind that reinstalling the system would replace all of the OS, so there’s no way to leave counter-measures there, and the disk itself can’t do anything to your data, even if it could detect a clone operation.
If what you’re trying to protect against is someone who knows everything you do accessing your data, you could look to use TPM to store the encryption key for your FDE. That way you don’t know the password, it’s stored encrypted with a secret key that is, in turn, stored and protected by your CPU. That way a disk clone couldn’t be used on any hardware except your specific machine.
This seems like a very complicated way to achieve your goal! It sounds like sitting yourself down and giving you a stern talking to might be a beter aporoach.
Having said that, if you have these very important files that you don’t want to lose, please make sure they’re backed up somewhere off of your machine. Storage fails, and it’s a horrible feeling losing something important. Unfortunately doing so would defeat the approach you’re thinking of.
This might be a case of needing to reframe the question to get to the cause of the issue, and then solve that. So, why do you want to make it hard to reinstall your machine? Is it the amount of time you spend on it, the chance of screwing it up, needing it working, has it become a compulsion or something else? Maybe if we can get to the root of the issue we can find a solution.
With regard to TPM, it’s basically just a key store, so you can use it fir anything really, althought it’s normally used by generating a TPM key and using it to encrypt the key that’s actually used to encrypt your data, storing the encrypted key with the OS. Just reinstalling won’t wipe the TPM, but unless you made an effort to save the encrypted key it’ll be gone. Given your problem statement above it just adds to the data you’d need to save, which isn’t helpful.