Ok so I made a small bash script to remove some Logseq specific formatting:

find $1 -type f -name ".md" | while read file; do
sed -i '/{{query/d' "$file" # This removes any embeds
sed -i '/{{embed/d' "$file" # This removes any embeds
sed -i '/{{renderer/d' "$file" # This removes any embeds
sed -i '/::/d' "$file" # This removes any tags/properties featuring ::
sed -i 's#../assets/#assets/#g' "$file"
sed -i 's/(([\a-f0-9-]{36}))//g' "$file" # This removes UUID like strings
sed -i 's/- (#+)/\1/g' "$file" # Removes "- #" Outline headers and replaces them with #
sed -i 's/{{video\s(http[s]?://[^}]*)}}/\1/g' "$file" #Removes the video tags
sed -i 's#(http[s]?://[^ ]*)#[\1](\1)#g' "$file" #Adds to any links that dont have it

done