I have file A.bat:

echo %%y > test.txt

however after it is ran test.txt contains only "%y"

Why does it keep omiting my second percent sign? and more importantly how do I stop it?

"the right to swing my arm ends where your nose begins."
-Claude Adrien Helvetius

Within a bat, one % is always 'stripped'.

What are you trying to do?

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If at first you don't succeed, you're about average.

M2

Echo %%%%y > test.txt

i.e. you have to double each % symbol as M2 pointed out. Better however you explain what you are trying to achieve to avoid waste of time and misunderstanding.

ahh, wow, I feel stupid. instead of thinking 2 to 1, I was thinking subtract one, so I tried:

echo %%%y > test.txt

and it did the same thing, I assumed it would continue in this fasion. But it doesnt. Thank you Ivo!

"the right to swing my arm ends where your nose begins."
-Claude Adrien Helvetius

You can also use the ^ (caret) symbol as an escape character.

^how might that help me mate?

"the right to swing my arm ends where your nose begins."
-Claude Adrien Helvetius

It gives you a second option:
echo %%%%y > test.txt
or
echo ^%^%y > test.txt