Im new to speedrunning this game, and I have put over 100 hours in my main save (which is on the most recent patch). I want to down-patch to speedrun the game, will doing so corrupt my saves?

Any help would be great, thanks!

If you don't enter your main save file with the downpatched version of the game then no, downpatching won't affect it. If you're worried you can back up your save file by copying the corresponding userX.dat file to a safe location.

=== Saves ===

Windows File Paths: (Assumes Default Steam Install Path, Adjust accordingly for DRM Free or Non-Standard Steam Path)
Save Files: %APPDATA%\..\LocalLow\Team Cherry\Hollow Knight\
Game Files: C:\Program Files (x86)\Steam\steamapps\common\Hollow Knight\

Mac File Paths:
Save Files: ~/Library/Application Support/unity.Team Cherry.Hollow Knight/
Game Files: ~/Library/Application Support/Steam/steamapps/common/Hollow Knight/hollow_knight.app/

Linux File Paths:
Save Files: ~/.config/unity3d/Team Cherry/Hollow Knight/
Game Files: ~/.local/share/Steam/steamapps/common/Hollow Knight/