How to manually invalidate a pull merge replication snapshot from the publisher
I looked in to the declaration of sp_changemergepublication and found out the way it invalidates the snapshot is a simple query to update the table sysmergepublications 

if (@property like 'ftp%' OR @property in ('sync_mode', 'snapshot_in_defaultfolder',
        'alt_snapshot_folder', 'pre_snapshot_script', 'post_snapshot_script','compress_snapshot','keep_partition_changes',
        'use_partition_groups', 'publication_compatibility_level'))
and @snapshot_ready = 1
begin
    if @force_invalidate_snapshot = 0 and @snapshot_ready = 1
    begin
        raiserror(20607, 16, -1)
        goto UNDO
    end
    update dbo.sysmergepublications set snapshot_ready=2 where pubid=@pubid and snapshot_ready=1
    if @@ERROR&lt;&gt;0   GOTO UNDO
end


So if you want to invalidate all subscriptions and snapshots just run these two lines.

update dbo.sysmergepublications set snapshot_ready = 2 where snapshot_ready = 1
exec sp_reinitmergesubscription @upload_first = 'true'