When an auto report source member (type RPT or RPT38) is detected in an RPG III or OPM RPG/400® source program, the Conversion Aid calls the CRTRPTPGM command to expand the source member and then converts it. (This is because auto report is not supported by ILE RPG.)
The auto report program produces a spooled file each time it is called by the Conversion Aid. You may want to check this file to see if any errors occurred on the auto report expansion, since these errors will not be in the conversion report.
In particular, you may want to check the auto report spooled file for an error message indicating that /COPY members were not found. The Conversion Aid will not know if these files are missing. However, without these files, it may not be able to successfully convert your source.
Auto Report supports compile-time data in /COPY members. RPG IV does not support this. If you are keeping compile-time data in /COPY members so that several programs can use the data, consider moving the compile-time data to a user-space and accessing it through the user-space APIs.