It is not clear that it is a serious problem, but you may want to choose a different CVS mirror to conduct an update or a second checkout. From my brief research it is associated with the internal CVS/Repository files in each working directory that are created during checkout, and not with the checked out data itself.
Please see src/gnu/usr.bin/cvs/src/client.c, which produces the message, and then see the discussion of the warning in src/gnu/usr.bin/cvs/src/sanity.sh.
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