Synchronize and autosync 

The synchronize button on the bottom of your dashboard allows you to sync manually with the exchange. If there are coins on the exchange that are not shown in your Hopper, you are able to import them into your Hopper with this button. The imported coins could be used for new orders after selling them for your base currency.

Synchronizing positions is useful when you are missing coins that you see on your exchange, but not on the Hopper. 

What if I have small positions that I can't sync?

Having small positions that don't respect the smallest margin allowed in the exchange, can't be synced.
They can be scrubbed, however! Using the wallet scrubber can help you get rid of dust. Read more about the wallet scrubber here!