Huh? Where else are they used?
You mean third party apps like block explorers etc?
The actual four individual bytes are defined only once in the entire code.
Change them there and all parts of the code using them use the new values.
True, but how is that going to change this magic value in the user data files? I admit I could only look at the code briefly, but it appeared that the magic value is not only used in the network protocol. Also, as you mentioned: block explorers seem to require the (correct) magic value, hence I assumed changing it in a fast shot will invalidate the (disk stored) block chain.
You did not answer the question about whether you copied one other coin's unique magic bytes or copied the same ones it had already not made unique, so that maybe you and who-ever you copied from both are going to run into this collision of networks problem.
From where did you copy them? Had they made theirs unique?
-MarkM-
I forked form Litecoin (see first post, github link).