I ran once using comma and once using separate -y. I noticed that the header was slightly difference in # / TYPES OF OBSERV of the .OBS was wondering if you can tell which one is correct.
Using
./convbin -r ubx -f 1 -y E,C /home/patrick/Downloads/roof5APPGOODtest/base4/b4.UBX
4 C1 L1 C2 L2 # / TYPES OF OBSERV
./convbin -r ubx -f 1 -y E -y C /home/patrick/Downloads/roof5APPGOODtest1/base4/b4.UBX
Your output looks like the difference between -f 1 and -f 2
If you really didn’t change the f parameter, then you may have found a bug. C2 and L2 observations are for dual frequency receivers. They do not need to be enabled for logs generated by Reach devices.