You might have meant:
A naive merge would just paste Sonic3.bin + SonicAndKnuckles.bin. That crashes instantly. The working .bin file requires a custom header that fools the Genesis into thinking the lock-on initialization has already occurred.
Creating a single .bin file that works without physical lock-on is a nightmare of reverse engineering. Here is how a properly configured sonicknuckleswsonic3.bin accomplishes this: sonicknuckleswsonic3bin file work
If you clarify what you want to do with the .bin file (edit levels, change music, extract sprites, combine ROMs, fix checksums, etc.), I can give more specific steps or tool names.
You complete Carnival Night Zone, but upon resetting, your emulator forgot you collected the Chaos Emeralds. You might have meant:
The original cartridges used lock-on technology. In emulation, people sometimes merge the two ROMs into one combined .bin for convenience.
If you have acquired a file named sonicknuckleswsonic3.bin, here is how to verify its integrity: A naive merge would just paste Sonic3
Step 1: Check the File Size A proper merged ROM is not simply 4MB + 4MB = 8MB. Due to shared assets and bank switching, a working file is typically 6,291,456 bytes (6 MB exactly).
Step 2: Run a CRC Checksum
Using a tool like ROM Cleaner or md5sum:
Step 3: Emulation Testing
Load the .bin into Kega Fusion or BlastEm.