Yes, you can. Scenario 1 information is already 'saved' but that´s it if you continued with teh Sc1 save.
By what I understood, you have a Sc2 COMPLETE but that one was started without Sc2 DATA isn´t that right? If so, you won´t get for example, Spiriel as by default, she is killed on Sc1 battle... as well you won´t get the Justice Sword ( Save all refugees on Sc1 and 2? ) and you´ll get the sword on Sc3. I hope that was clear.
Of course, what you have done in Sc2 ( still without save from Sc1 ) will affect Sc3, like if you killed Stella or not..
Thanks, by the looks of it, Sc2 will be done about the end of summer or before, depending on legalize freedom and Atolm ( only translator )