A digital computer implemented software system is provided for enabling on-line programming changes of industrial logic controllers using a software package of the type utilizing graphical flowcharts is provided, allowing a user to modify a program and transfer industrial process state information while the program is controlling equipment. A control program has predetermined stop points of execution. Each stop point is assigned a unique index used to retrieve instruction addresses from an array. Each stop point also is associated with industrial process state information. By substituting new addresses pointing to stop points in a new program for the executing program addresses and transferring the state information, the executing program is replaced by a new program when execution continues on the next CPU scan. On-line programming changes take effect by replacing the executing code when all programs have reached a stop point, and by restarting a second program from the corresponding stop point in the second program.