If you start by making your code strict complient and add error checking to your IO, you'll likely fix some of your problems.
However, the likely main problem with your program is it's design. Your confusing use of Tie::File, intermediate lists in flocked files, duplicating large arrays, and global variables.
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?
"Science is about questioning the status quo. Questioning authority".
The "good enough" maybe good enough for the now, and perfection maybe unobtainable, but that should not preclude us from striving for perfection, when time, circumstance or desire allow.