Yes, I closed the files, but just to be certain I've just done the following:
1. Closed all the *.js.aspx files, quit Geany and restarted it by double-clicking one of the files (Geany is set as the default handler).
2. Opened another file by dragging and dropping into Geany.
3. Opened a third file by using File ‣ Open.
4. Copied an existing file via the file manager to create a copy with a filename that Geany has never seen before, then opened it via drag and drop.
5. Copied a file onto my local machine (they're usually opened remotely over SMB) and tried opening by dragging and dropping.
6. Closed the file, quit Geany, double-clicked the local file.
7. Closed the file, quit Geany, Relaunched Geany from the MATE Applications menu then loaded the local file using File ‣ Open.
In every case the file opened as XML. I think I've covered all the obvious options there, and ruled out loading from SMB as an issue, but if there's anything else I should try, please let me know.