@Lunos did you apply just the mega evolution patch or also the DNS patch at the same time? I also do not get the error by applying just one of the two patches.
However, I tried it with a clean base with both these removal patches applied and I can confirm that I got the same return-to-warning-screen problem in the first rival battle that Trev got.
As I said, Leons Ultimate Rom Base.ips and Remove Day and Night.ips were the only 2 patches I was using at first. Then I ran the ROM to see if I was able to confirm the freezing-in-battle issue, but I wasn't able to.
Then I applied Remove Mega Evolution.ips, checked again but nothing, the game is still working perfectly fine in both, VBA-M and mGBA.
The video which I recorded to show the issue with the DNS Removal Patch only has Leons Ultimate Rom Base.ips and Remove Day and Night.ips though.
Now, what I personally checked was wild battles, not the first rival battle.
I'm gonna do some tests again and will edit this post with the results.
EDIT: Alright, I'm done. I really wasn't able to trigger this freeze you guys are talking about :/ ...
VBA-M SVN r877
Leons Ultimate Rom Base.ips: The first rival battle is working correctly.
Leons Ultimate Rom Base.ips+Remove Day and Night.ips: The first rival battle is working correctly.
Leons Ultimate Rom Base.ips+Remove Day and Night.ips+Remove Mega Evolution.ips: The first rival battle is working correctly.
mGBA v0.7-5171 (latest nightly)
Leons Ultimate Rom Base.ips: The first rival battle is working correctly.
Leons Ultimate Rom Base.ips+Remove Day and Night.ips: The first rival battle is working correctly.
Leons Ultimate Rom Base.ips+Remove Day and Night.ips+Remove Mega Evolution.ips: The first rival battle is working correctly.
EDIT2: Jfc, I never noticed how washed out the colors were in VBA-M compared to mGBA, just like at that textbox and the font o_o ...