As of writing this, from testing, it seems that running on a completed profile is better for speedrunning as running on a fresh profile seems to slow the game down quicker. However, if you would like to test runs on a fresh profile or we make any future breakthroughs, you can reset your save by pressing Win+R (or just using your Windows search feature) and pasting in:

%APPDATA%\Macromedia\Flash Player\#SharedObjects\

Some people might have a single folder here, whereas as others might have more to navigate through, but the file you're looking for is "polinko.sol" (using myself as an example, I would paste the above search, then click through the folder there, and then go to the "www.kongregate.com" folder where "polinko.sol" is).

The "polinko.sol" file is the save file, so just delete this, or move it out that folder if you want to back it up, then run Flashpoint and Polinko again and you'll be on a fresh profile.