Synchronization of your Brain is very time sensitive. The most important rule to remember is that each individual Thought will default to the most recent change. This means that if I edit a Thought note on Machine A on Monday (does not matter if it's a desktop, iOS, Android, etc.) and I don't sync. Then, I edit the same note from Machine B on Tuesday, and again, I don't sync. When I finally sync ALL machines on Wednesday, only the Machine B, Tuesday edits will exist on this specific note. TheBrain sees that the Tuesday edits are the most recent, so it overrides any previous edits.
Therefore, it's a great idea to set your Brains to auto sync on the desktop. On mobile devices, you'll need to remember to tap the sync button often. Auto sync for mobile devices is on our feature request list.