To convert airplanes of version 3.0 format to version 3.5 format, simply run the convertor program ("convert 30 to 35") and select an airplane to convert. The program will then convert it and quit.
You will see the airplane in the same folder as the convertor application with a name like "Baron35.acf", meaning that it is file format for version 3.5. You can then change the name of the airplane and throw away the old airplane file if you like.
Note that FLOATS and ARTIFICIAL STABILITY SSYTEMS will NOT be converted, due to differences in float and artificial stability simulation.