This sometimes happens with lots of small incoming funds from mining.
The first thing to try is launching Agama with the rescan parameter
If you are comfortable with Command Line Interface (CLI) use the following command -
z_mergetoaddress ["*"] "destinationaddress"
Replace "destinationaddress" with the address you want the merged funds sent to.
The above command can be done in a terminal window, or by using the CLI tool in Agama desktop
If you are still having trouble, head to the Pirate website at https://pirate.black/ to get links for their Discord / Telegram channels and a community member should be able to assist further.