vinyl: fix for deferred DELETE overwriting newer statement

A deferred DELETE may be generated after a newer statement for the same
key was inserted into a secondary index and hence land in a newer run.
Since the read iterator assumes that newer sources always contain newer
statements for the same key, we mark all deferred DELETE statements with
VY_STMT_SKIP_READ flag, which makes run/mem iterators ignore them. The
flag must be persisted when a statement is written to disk, but it is
not. Fix this.

Fixes commit 504bc805 ("vinyl: do not store meta in secondary index
runs").