The standard way is to set up a complete set of app data, upload it and activate it. There would be no restriction then.
As a sub sum of this you could only exchange the PLC folder in the app data set. Control hast to restarted after exchange (or at least switched in service mode and back up in operation mode)
The lowest level would be exchanging only the application files. That comes with some restrictions:
The set size of retain data useable for the PLC must not be changed
Name of the PLC application must not be changed
Folders cnc, visu and plc must be empty (no Codesys visu cnc or so on is used)
Other data used by the project are not changed e.g. csv files...
Control hast to restarted after exchange
Project data is not changed ("new" PLC project cannot be opened from the control)
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