I ran into issues comparable to the issue discussed here.

When I use the "resolve using mine" or "resolve using theirs" functionality in SourceTree, I end up with a file on the local workspace that still contains the conflict markers, as can be seen in the SSIS snippet below:

<SSIS:Property SSIS:Name="Sensitive">0</SSIS:Property>
<<<<<<< HEAD
                <SSIS:Property SSIS:Name="Value">ConnectionStringA;</SSIS:Property>
=======
                <SSIS:Property SSIS:Name="Value">ConnectionStringB;</SSIS:Property>
>>>>>>> hotfix/20170403
                <SSIS:Property SSIS:Name="DataType">18</SSIS:Property>

As opposed to the other issue I referred to, it's not Visual Studio holding on to an earlier version, as I opened the file in a separate text editor straight from the working folder on the file system. The markers definitely appear in there, rendering the SSIS package entirely corrupt when opened in Visual Studio.