@Earthling45 : Indeed, this is the current state and I think it ticks the most boxes. As we are now, old levels still load for everyone, broken assets are fixed (thanks to GraPhiX, Myke and Teabone) and saved under the same name, no unnecessary duplication of content and overall, a much improved Mega Pack 3.
I have not tried it, but for users who want the very old and original Mega Pack 3, I think you can revert to an earlier build of GameGuru via the Steam betas tab and this should restore the MP3 files to an earlier date. Not that I am recommending this, the latest one is definitely better with just a few outstanding assets that require a little more time to correct. If you want to see specific fixes to Mega Pack 3 you are welcome to post them with screenshots and entity name references to the Issues Tracker and also feel free to donate to the Asset Fixing pot, as we use this to help pay for contributions to the artist community.
@GraPhiX: Aside from the RUIN asset sequence, are there any other MP3 assets in there you feel should be addressed? Mega Pack 3 has been a good template for figuring out the workload required to update a Mega Pack, and with hundreds of hours already put into MP3 alone, it might be an idea to just leave MP1 and MP2 alone and as you suggested with an MP4, just place updated content in a new pack or folder in future?
PC SPECS: Windows 10 64-bit, Intel Core i7-8700K, NVIDIA Geforce GTX 1080 GPU, 16GB SYSTEM RAM