Just another user having what appears to be the exact same problem!
This all started for me when I updgraded my Macbook Pro to the Sierra OS. Prior to this Endnote had no issues at all despite my library containing close to 2000 references, many of them quite large PDF documents.
Some notes:
Crashes appear to occur at random. They may happen an hour into me opening Endnote, or in the first few minutes. Oftentimes, endnote will simply be open in the background and when I go to insert a reference I will find that it has hung (pinwheel of death)
The only way to get Endnote working again is to force close and reopen.
Crashes happen for me typically anywhere between 5 and 15 times per day. This is INCREDIBLY FRUSTRATING. Seriously thinking of moving to a new referencing platform.
Please help!!!