You may experience current workflows are being suspended and no longer running to completion. This is due to numerous deleted association workflows that are ahead of the new running instance. 

This is a known issue with 2 possibility of the root cause:

1. There are other workflow on the list (if any) to make sure that all the workflow has a Start Option from Workflow Setting (at lease one of the option checked). If all the workflows has the start option, then it related with Microsoft issue that lead us to possibility no 2. 

2. Most likely the issue down to a problem with the workflow publishing location associated to the specific site library. Workflow definitions are normally stored in a hidden folder called "wfsvc". This issue creates another folder called "wfsvc1" and puts the workflow there - Microsoft should be able to move the workflows from the wfsvc1 hidden folder to the wfscv hidden folder then remove the wfsvs1 folder. In some cases republishing the workflow may resolve the issue if not you will need to contact Microsoft for addition support.