CRLF and LF are variations in line endings for different Operating Systems, and thus the formatting difference might be due to two different people accesssing the files using different operating systems: Windows vs. Linux for example.
Both the .cyacd files were generated in Windows OS using PSOC creator. Then I copied these files to Linux OS. Then when I checked the line endings, one file ended with LF and another with CRLF. I am not sure why. I am observing differences in same OS. Not sure why.
Windows uses CR/LF, and Linux uses only LF I believe. I would ignore the line endings being different; It's not really relevant to any of the compilation/code/hex data for the end of file formatting.