Ignoring CR is often how two systems end up parsing the same file differently, one as two lines the other as a single line.

If the format is not sensitive to additional empty lines then converting them all CR to LF in-place is likely a safer approach, or a tokenizer that coalesces all sequential CR/LF characters into a single EOL token.

I write a lot of software that parses control protocols, the differences between the firmware from a single manufacturer on different devices is astonishing! I find it shocking the number that actually have no delimiters or packet length.