If both are deployed, there won't be any conflict. The rollups only update any out of date components necessary.
If you deploy the Monthly rollup, and then manually install Security Only, nothing will happen.
If you deploy Security Only, and then Monthly, the non security portions of Monthly will be installed.
We tested this and confirmed no files are changed when deploying the Security Only update after deploying the Monthly rollup. Therefore, if you deploy Monthly in Protect, when you scan that machine, the Security Only rollup will show up as "Effectively Installed".
Seems like an unnecessary hit on network bandwidth.
Additionally, since these are both classified as Non-security patches with a Vendor severity of Critical, how can we easily set our templates to scan (and deploy) for just one or the other without having to manually exclude one each month?
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You can filter by Security or Non Security in those scan templates to exclude one or the other. They aren't both security - The Security Only bundle is Security, the Monthly rollup is Non Security. I've added screenshots below of both rollups demonstrating this. CR16-001 = Monthly cumulative rollup. SB16-001 = Security Only rollup.