When you use DropBox as a data container before the DevonThink 2.5 version, when you use differents Macs adressing, one after the other, the same database, this database becomes more and more corrupted with time.
html or text files names continue to appear in your lists but with nearly no size (some hundred bytes). If you open them, you will see that they are empty (the content has disappeared).
If you have a look to the content of your database, you will see metafiles (.dtMeta) in confictual situation .
If you do not delete these conflictuel .dtMeta files and if you do not delete or rebuild the .txt and .html files, you have no chance to sync.
Tipically, you will have a message explaining that a file is empty (content = null), that the sync has failed, that it has no more internet access, and so on… 
So backup your data first and then delete what is corrupted followin these instructions (Arnow is the author) here: