When you run the beta over an existing 5.0 installation it will change/add data to the config.ini file and rename the user notes file. If you then run the 5.0 version again, it will rewrite the config.ini file because it can't understand the new data in the modified one.
v5.2 renames the v5.0 notes file from notes.usr to default.nts. It also makes a backup of the notes. For v5.0 to see them again you will have to rename it back. v5.2 allows multiple user notes files is the reason for the change.
Other than a default config.ini made when v5.0 is run again and the note file renaming, there is little else changed in the file system.
Developer, Bible Analyzer
But to him that worketh not, but believeth on him that justifieth the ungodly, his faith is counted for righteousness. (Rom 4:5 AV)