Proper way of handling Cache Conflicts

Hello,

I wish to ask what is the best way on dealing with plugins that are changing files outside of the IDE. It looks like accessing directly the VirtualFile and writing their content results in possible Cache Conflict dialog to popup. 

Is there a way to write the VirtualFile that will make sure that:

1. Is up to date with the in memory representation.

2. Would cause a sync between the file system and memory state without need for user manually resolving the Cache Conflict.

I would hope for an user experience that is very similar to the one that the "Reformat Code" option triggers across the entire directory tree structure and make that as seamless as possible to the end user.