>> Once I installed 12.1 RU6 on my production SEPM (it's been about a week now) I started getting this message from the SEPM along with a listing of the machines requesting full downloads (usually about 30 machines).
I had the same here.
>> Will increasing my content revisions help the situation?
Most probably not. See following remark.
>> Will the alerts eventually subside once all the machines have "caught up" with the latest definitions?
Yes most likely. This is what happened here. When you check the report on type "Computer Status" and select "Protection Content Versions" you see a selection of 8 components, all having dozens of different version numbers live in your environment.
1. To me it appears that pre-12.1.6 updates of engines and definitions for all components EXCEPT Antivirus were flawed. Not coming through via SEPM. Sometimes, I was able to run LiveUpdate on the client to get updates of engines and/or definitions that they couldn't get from the SEPM. LiveUpdate is a backup-mechanism and should never have to be run, it contacts the symantec servers directly, bypassing SEPM. But even that didn't work on all my clients. Weird. This looks solved now with 12.1.6.
2. A second thing I presume, is that 12.1.6 has another component that wasn't there before. So every (12.1.6) client needs a full download for these components before it can start using delta's. These are the only 3 "items" that I got this critical alert for:
= SEPC SMR Definitions 12.1 RU6
= SEPC SRTSP Settings
= SEPC Virus Definitions Win64 (x64) 12.1 RU6
So my advice:
1. absorb the alerts during upgrade if you can (it looks like so);
2. if not, spread the upgrades, either by using the "Upgrade Schedule" in the "Client Install Package"s to distribute the upgrades over more days; or;
3. do bit by bit; e.g. do not use the "Instal Package" in large client groups, but create a new group called "Do SEP Maintenance" with the 12.1.6 install package and move (or copy if you use AD synced groups) clients batch by batch to the maintenance group (and back again after their upgrade).