Flare Build Batch File Restructuring

[TheBrittleTechWriter]

I am trying to use a custom tool to create a batch file to build specific files. However, whenever I open that file, Flare overwrites my contents with its own, and includes all the files.

To be clear, on opening the file through the Flare UI, the file's content is clearly ignored and the UI displays whatever it wants to. If you change something and save the file, at that point it overwrites the original content.

Can I make Flare display what I put in the file?