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Is there a preferred method for this, or is it fine to simply delete every track?

Since hard disk trouble is suspected, then please do a full "Builder image" wipe, including the stress test, as described in the Disk Upgrade Guide.

Be sure to read the instructions carefully, especially the part about needing to press Enter in the shell to get it to actually build the disk (it's going to say disk is already built).
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Tony Fabris