To be honest I don't know if it might be related to my problems.
The module in question is throwing Orchard.Environment.Extensions.ExtensionLoaderCoordinator - No loader found for extension "MyModuleName"! all over the log and crashing whole website. The only thing that I've noticed that differs
between my other custom modules is this .deleted file in dependencies.
Note. That when I rebuild the project everything works fine - for a while.