Hello FPhil,
To the question of updating 69 files, the answer should of course be YES. Updating files manually or automatic invokes the same procedure, therefore has the same net effect (if answering YES).
VemsTune program changes (as available on:
http://vems.hu/download/v3gui/) are only made when there are changes to the program itself (executable or underlying database structure), rest of the updates are available through update server (ini_update) this also counts for the latests dialogs and menu help files.
The integral increase/decrease limits are limits of the integral itself (the sum) to use your analogy, the errors are not being summed anymore when reaching either of these limits.
Secondly there are also absolute limits on the total output (Reference + PID) which are in "Idle PWM/Stepper Hardware settings", "Max/Min PWM/Steps Allowed" again using your analogy this is a limit on max output value, errors might still be summing up if integral limit is not yet reached.
If there is anything still unclear, please let me know so i can elaborate further in help to make it more clear for everyone.
Best regards,
Dave