Reproduced with the MSPM0L1306 out of box demo project, but most likely any non-sysconfig project will reproduce the issue. 

Import nonsysconfig enabled project, 

Right click on import project and choose System Configuration-> Create New

There should be a pop up asking to convert to a sysconfig project. 

Double click on empty.syscfg file, there will be an error and then a new file sysconfig panel to choose sdk, board, etc. Pick MSPM0L1306 LaunchPad

SysConfig opens with modules, add a module and choose File->Save

Dirty icon disappears, but checking file system, empty.syscfg has 0 size. 

Closing sysconfig and opening it in Code Editor (Open With -> Code Editor) shows that it is empty.