I'd guess yes, and you get the SQL goodness to boot :)
Sounds like you have an encoding issue somewhere, windows has it's own charset - Windows-1252, so I'd vet all your libs that touch the file (including eg. .Net libs etc). If one of them defaults to that encoding you may get it either mislabelling the file encoding, or adding in null after each append etc.
SQLite is tested cross-platform so 100% the file will be cross-platform compatible.
Sounds like you have an encoding issue somewhere, windows has it's own charset - Windows-1252, so I'd vet all your libs that touch the file (including eg. .Net libs etc). If one of them defaults to that encoding you may get it either mislabelling the file encoding, or adding in null after each append etc.
SQLite is tested cross-platform so 100% the file will be cross-platform compatible.