I have a script which, each time is called, gets the first line of a file. Each line is known to be exactly of the same length (32 alphanumeric chars) and terminates with \"
You could store positional info into the file itself. For example, the first 8 bytes of the file could store an integer. This integer is the byte offset of the first real line in the file.
So, you never delete lines anymore. Instead, deleting a line means altering the start position. fseek() to it and then read lines as normal.
The file will grow big eventually. You could periodically clean up the orphaned lines to reduce the file size.
But seriously, just use a database and don't do stuff like this.