So just to explain what the issue is a bit more.
There is a NetSuite limitation that if the transaction sublist (e.g vendor payment sublist) has more than 10K lines, the additional lines are not available.
However, the sublist headers have toggles, and you can customize the sublist as a user, but unfortunately, it seems for MR scripts, it'll always execute as the system user. This means that you cannot customize the sublist and overcome the issue. What I'm saying is running the same snippet of script in the debugger will yield different results (the lines displayed on the sublist is different, and if it doesnt appear on the sublist, it cant be selected.)
In this specific case, it seems that a mass update script when executed will run with the user settings... So in the end I refactored the script from MR to mass update. Executing the script as mass update aligned with the same lines that could be tested on the debugger