Deparse is not perfect and it tends to develop new bugs with new perl releases (because the structure of the optree gets changed without always remembering Deparse). It also has large areas such as closures where it just won't easily work. It also will strip all comments and pod (including copyright statements or licensing terms, which may be a legal issue).

Update: if it is any comfort, when Deparse breaks it usually breaks badly enough to get noticed and fixed before a perl release. And it probably is your best bet for accomplishing the job (with the possible exception of figuring out some way to use AutoSplit.)