Hello GrinGEO,
Usually the folders with additional indices (like elevation.1, elevation.2 and etc) appear when some operations with the named instance are performed - so the old object is kept and the current operations are performed with the temporary duplicate. If the project is saved, the old element is removed and the new one is put to it's place.
The connection may be lost, if the save operation hasn't been completed properly, the project has crashed or unexpectedly closed. So in order to fix the issue we need to understand which steps are causing this behavior.
All paths to the project instances are kept in the doc.xml file inside the frame.zip archive (at the bottom level of the .files folder, like: project.files/0/0/frame.zip), so you should be able to see there which elements are linked with the project and under which paths, just for case you need to correct them manually.