Problems with automatic updates on indexed folders

Hi, there. I’m having trouble with my indexed folders on Devonthink3 Pro.
The problem is:
I have a database with a main indexed folder and many nested folders under it on an external ssd. For most of the time, DTP3 does recognise nested folders and files, but sometimes, a few of these nested folders do not update automatically. A manual update did solve the problem but the next day the same problem could happen again.
What’s get weird is that not all the folders fail to update, some do, some do not.
So, could you please help me with that.
English is not my first language, apologise for any confusion in my post.

Is this external SSD always connected to the same computer and mounted?

Welcome @jackhanson
Are you using some process or application to sync the data in that drive, e.g., Resilio Sync or similar?