PLCnext Engineer deletes working files

Hi,
Using 2025.6 I have encountered an annoying problem that manifests in two different ways:

  1. PLCnext engineer suddenly deletes all files in my working project (a flat project, all files in the /content-folder)
    It does not warn me of anything, and the only way I am noticing it is by trying to save - where I get an error that the project cannot be saved at this location (or any other location if I try that).
    I see that the files are being deleted by watching the git status, where it lists around a thousand deleted files. Some times I can salvage the situation by restoring the files (i.e. discard the file change using git) - some times not. I have lost countless hours of work this way over the years - because this particular behavior I have encountered many times over the years, at least back to version 2023.

  2. The new error is that some files are being deleted. The project can still be saved, debugged and everything seems flawless until you close and reopen the project and a strange list of errors appear in the log:
    image.pngThis is because PLCnext Engineer has deleted these files:
    image.png(This is a screenshot from my git client, showing that a file has been removed from the repo).

It is quite tiresome to restore this error, as I have to roll back a few commits, and later cherry pick working files to restore my work.

Please forward this to the development team because this is not acceptable.

Here is an example of PLCnext engineer deleting all files:

image.pngimage.png(note, 1116 files are being affected, all but two are removed)

The Structure.xml files is wiped clean:
image.pngThe safety file has some additions (there is no safety project in the program):
image.png

I also noticed now that when the project only deletes some files (and generates these four error messages), it also wipes them from the structure.xml:

image.png

Hi fluxmodel,
We will speak next week in a meeting with the development about this topic.
Thank you for the detailed report.