The same problem arises in respect of the kernel upgrades (needed to patch Meltdown vulnerabilities) that have to be done in the terminal.
For now I've updated in Gslapt on a piecemeal basis certain user-facing apps like Firefox, exaile, flash. But for the kernel upgrades at the very least, will it be safe to follow the terminal directions to override:
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Missing MD5 checksum, override with --no-md5