You'll still be able to access your tree. You won't be able to view any records you've attached to it if you've attached only links. You should download any records to your computer that you might wish to view or use later.
You can use the description fields for records to make notes about the information they provide, including pointing out differences between various records for a given person, and whether you feel the information is conclusive or more research is needed. The description field is rather limited in the amount of text you can put in it, though. You can use the "stories" feature to record more lengthy notes. Other researchers may have other helpful suggestions so you'll need to see what works best for you.
Happy hunting! :)