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Unexplainable data loss

I have an HP Elitebook that is currently fitted with a 2.5-inch SSD as the main Windows 7 drive, and a 1TB mSATA that contains working files and a majority of VirtualBox images as both VHD and VDI files.

I have recently swapped out the 2.5-inch SSD with another one and installed Windows 10 on it, which has gone very smoothly apart from one issue: When I swap back to the Windows 7 SSD I notice that I have lost some VDI files completely, and others have been corrupted.

I have managed to recover some of the lost files from backups and have tried the swap again, and the