I can’t download the second project because dropbox says it’s too large.
I suspect the problem is that you applied the Low Pass Filter to the entire project in one go rather than to one track at a time.
“Nyquist” effects (the Low pass Filter is a Nyquist effect) cause selected empty track space to be rendered as silence, so if you select the entire project and the start/end times of all tracks do not match, then the selected “white space” (empty space) will be converted to “flat line” silence, which will then be included in the export.
The solution is to process one track at a time so that you only select the actual audio and do not include leading / trailing silence.