We have two paid Express Invoice programs, on two separate computers. We utilize their sync through Dropbox feature and it works quite well. I know that doesn't answer your question directly, but it is something for you to consider for the future. We did it this way because both of our users much prefer the computer version rather than the web access. It syncs all the behind-the-scenes settings and the data input. The only problem I've had with it is that it doesn't seem to carry over the customized field.
To answer your question, I am not sure, but I have a feeling it will overwrite the current data. Perhaps you could do a trial by starting a separate company, inputting some data, and then import the old data to see if it overwrote the existing info?
I would be sure to back up your current info no matter what you do!