Linked files disappear from source project

[Esther]

Hello,

This is an issue that just started happening last week and I cannot understand why. In brief, when I reimport files from a source project into an existing project, Flare deletes the files from the source project.
Below is the way the projects are set and the issue that I am facing:

Background
* We have 65 standalone projects; each project represents a "guide."
* We have a single Release Notes project.

Procedure
1. As content changes in our guides, I create a Flare Project Import File and select the file(s) that I want to import.
2. I import the files and add them to a review TOC.
This process has been working fine for three years now. Just recently, when I re-import the files into the Release Notes project, Flare deletes the files from the source project!

Workaround
As a workaround, my colleague disabled the Auto-reimport before "Generate Output" option and that seems to have stopped Flare from deleting the files in the source projects.

Any idea what's going on?
I attached the Import project screen shot for reference.

Thanks,
Esther