MEDICAL RECORDS: Unable to load medical records from CD when patient transfer to our office because file is too large.

Our office is receiving a lot of patient records transferred from their old office. The disk normally contains one PDF file with the entire chart. I would like to upload the contents into eCW patient documents but am unable to do this because they are almost all over the 3MB limit. I am pretty sure that all of the emr systems create one pdf document when providing medical records. I know that is how ecw does there records. BUT it is impossible to upload these files to the system. I have contacted eCW “support” (and I use that word very losely , and they say there is nothing they can do about it. Does anyone have any suggestions on the best way for me to handle this issue. I am very new to using electronic medical records and can use some help and ideas from more seasoned users.