1. First upload (with no program in computer memory);
2. Then Import from the old stored program.
PS: Because you were prompted while trying to go online does not mean that there are any significant differences between the PLC program and the stored version. It can be something like a differnce in 2 data values that Harryting pointed out, or simply a program that was stored at a different time.
To spot major differences, use the Compare function that easily lets you see and step through the differences one at a time. You can also sometimes tell by looking at the program memory size, the number of subroutines, and the last "B3" or "N7" bits used in each program.