I'm not sure of this. But wouldn't it be better trying to link up the saving and counters in some way? Maybe post some of the code to get a better idea of what the problem is.
A simple fix might be by using LevelFilename, haven't used/tested it, but i would imagine the output is the name of the current level. So..
if LevelFilename == "level1" then
and reset the counters in the text doc.
I'm new to this so take it with a pinch of salt.
This fix has issues with it I am noticing now, such as if a player loads a save file on level 1 the counters will also reset I think. And it can still be abused on later levels with save files. But I'm still gonna post this as it is a place to start at least.