I have been using Mendeley for a very long time now. I use it for organizing and reading articles. I just noticed that it keeps removing files randomly from the folders and groups. I don't know the exact reason for this. I wonder if there is an alternative to the Mendeley desktop client for Windows.
Zotero is a free (and open source!) alternative: https://www.zotero.org/
There is a plenty of other tools (just google 'citation managers'), but I believe that Zotero's open source nature renders it preferable to all alternatives - including Mendeley, which belongs to the large commercial publisher Elsevier.