If it were me, if you are POSITIVE the online tree is of no use to you, delete it. But ONLY if you know you have everything you need from it.
I would then upload and sync your tree from FTM. You may have hit the upload button once before and thats why you have the tree online. You can upload without syncing.
Sometimes it may look like your tree didn't upload 100%, but this is probably because media is still processing or something. Give it a good day before you start to question if it uploaded completely or not.
You can get hints for a tree you just have on FTM. There's a preference in the settings that lets you toggle this on or off.
You should be fine if you have backups and exports like you said.