If changes are not significant, it's better to put modified css rules to css/custom.css (without leading underline).
If changes are significant, maybe it's better to:
1) copy templates/mobile_basic to templates/mobile_basic2 (or some other name),
2) change new template name in templateDetails.xml appropriately,
3) go to Extensions->Discover and Install new template,
4) and switch to new template in MJ settings.
After that updates of MJ will not affect your modified template.
PS. As to your issue, it is due to change in js merging algorithm and will be fixed in 2.1.24 soon (in few hours).