Please clarify the following:

1. When you said  "it brokes the files for all devices in the main group",  did you actually mean "all 40" devices that were moved to the main group?   Or all devices, including those that had been in the main group before you moved the 40 devices?

2. Did you duplicate a new set of rules for your "test" group based on the old set of rules for your "main" group?   Or did you just change the rule target of the rules for the main group  to include also your "test" group?  

3. Is your "test" group a child node of the main group? 

4. What advanced options (persistent, re-install, etc.)  did your set for your package deployment rule(s)? 

5. What options did you set for the pcg package included in your package deployment rule(s)?

1. It broke the files for ALL the devices in the group, not just the ones I moved.

2. The rule target was changed to include both groups. 

3. The groups are both in the same root folder. 

4. The only options set in the rule deployment were to install immediately after download

5. The files from the packages in question were both marked to NOT be uninstalled when built in the Package Studio. That's what makes so little sense to me. Doesn't that mean that unless those files are to be overwritten, they should not be removed?

What you had for my question (1) did not make sense.   Did you change any option in the package deployment rule when adding the new "test" group as extra target? What about disabling and then re-enabling the package-deployment rule?  If not, then there must be something wrong in the server or agent binary.  What were the version and build numbers of the device agents on your problematic devices? 

Unfortunately, your server version of v12.3.0.28297 is rather old and I have no resource to do any quick test.  You probably need to open an official support ticket with Soti support team and let them look into your implementation in more details.  If what you experienced can be repeated on your server again,  it should be relatively easy to verify if the problem come from the server binary and whether there is any need to upgrade your server to a more recent version.

We are actively working with the management to update our software to the latest version, which I am excited about. 

Upon further inspection of the logs it looks like the rule was, in fact, disabled and then re-enabled a few hours later. I assume that would explain why it affected all the devices in that group. It's odd to me that they were removed at all since they were marked as "do not uninstall", but perhaps I missed something.

Either way, thank you for your help @Chan!