That is very strange. Spine doesn't keep the image files open. You can use something like LockHunter to verify this. Spine does monitor folders, but that should not prevent the folder from being deleted or renamed and won't affect writing images files in the folder.
Spine monitors the image folders so the OS can tell it when files change. When an image file changes, Spine notes its length and waits 150ms. If the file's length has changed in that time, it waits another 150ms and repeats. If the file hasn't changed, Spine reloads the image, which consists of opening the image file for reading, reading the bytes, and closing the file. This whole process should not interfere with AE writing images and hasn't changed from 3.6 to 3.7.
Does it happen with other programs (eg Photoshop), or just AE?
In our tests, we are able to modify image files just fine. What is the easiest way we could see the same behavior you are seeing? That would really help us a lot!