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i am terribly sorry to hear that!

please do not hit save in ardour before the issue is possibly solved... try to use "save as..." instead (if ardour supports it).

sample file references are stored as part of LV2 plugins parameters state, so it's kind of not-human-readable...
you can however look into audour's session directory or folder for respective symlinks: each sample file is referred to by a symlink to each and actual file location in your file-system, stored outside the ardour session directory; also check if the sample files are still there or moved away somehow;

i'm afraid that's how far i can help you at this time.
hope you find your way through it all

cheers