Assuming a user performs some changes in the file AppNamePortable.ini. Furthermore should be this particular program installed in the PA.com menu.
To preserve the manual changes made by the user in the settings during an automatic update of this program, it's necessary to note the following points:
The user must reapply at the new AppNamePortable.ini file the personalizations, which the user has performed at the old AppNamePortable.ini file. Of course only in the case, if these options are still present on the new AppNamePortable.ini file, and if these personalizations are not in conflict with the corrections applied in the new AppNamePortable.ini file.
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The AppNamePortable.ini file is not meant to be user-editted. Anything you change there will be wiped out on every upgrade. If an app is missing a feature of some sort (AppNamePortable.ini entry), please request it in the forums.
Sometimes, the impossible can become possible, if you're awesome!
Basically, however, the user has the possibility of changing the file AppNamePortable.ini itself. And I have no control regarding the usage of this potential opportunity by the user. And as you have mentioned, anything of such a change will be wiped out on every upgrade. And exactly for this reason I want point out to the only possible solution (which I described above) for the user in case of an upgrade.
There's no need to point it out. The whole App directory is off limits to users and will be wiped on every upgrade. Nothing new there. About the same if you were hacking a local app's installed file within Program Files and then it would be wiped out when the app is upgraded. There's even a readme.txt file within the App directory that states:
Nowhere is there any indication that AppNamePortable.ini is a user-editable configuration file.
Sometimes, the impossible can become possible, if you're awesome!
For myself are all your explanations understandable so far. But yet it could be a user make use of the possibility to change the file AppNamePortable.ini itself. And even if he has read the readme.txt file, that those changes are not required and nowhere is there any indication that AppNamePortable.ini is a user-editable configuration file. Still, he could change it. And only to this particular case I want point out and nothing more.