Missing statistics are stored in the "sysstatistics" table for each database. Look for "formatid" of 110.
For example:
select user_name(so.uid),so.name,ss.colidarray
from sysobjects so INNER JOIN sysstatistics ss
ON so.id = ss.id
where so.type = "U"
and so.sysstat2 & 1024 != 1024
and so.sysstat2 & 2048 != 2048 /* regular tables */
and ss.formatid = 110 /* missing statistics formatid */
One could write a "delete" statement based on the logic above and create a stored proc (while "allow system table updates" is set on) that could delete these rows from sysstatistics. The proc could accept a table name (and even a column name), or such that would control doing this for certain tables/columns, or all tables/columns etc.