"Accept incoming network connections" issue

Due to some graphic and/or code based changes, within programs like Dropbox, iTunes, jDownloader etc. (but mostly Java-based applications), the built-in firewall keeps asking for verification.

Obviously, the code-based signature changed with my manual changes and that is the reason for firewall to point out this issue, which is a good thing: it shows that the security mechanism works. But the annoying part of it is that firewall doesn't remember the user's choice once it is made after raising the issue in the first place.

Does anyone have a clean solution for this problem? How can I assign the new created signature to firewall preferences?

localhost:~ Username$ codesign -vvv /Applications/Dropbox.app

/Applications/Dropbox.app: a sealed resource is missing or invalid
/Applications/Dropbox.app/Contents/Resources/!dropBox/box.icns: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy-lep.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy-lep2.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy2-lep.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy2-lep2.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy2.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy3-lep.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy3-lep2.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy3.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy4-lep.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy4-lep2.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-busy4.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-idle-lep.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-idle-lep2.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-idle.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-logo-lep.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-logo-lep2.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-logo.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-x-lep.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-x-lep2.png: resource added
/Applications/Dropbox.app/Contents/Resources/!dropBox/dropboxstatus-x.png: resource added
/Applications/Dropbox.app/Contents/Resources/box.icns: resource modified
/Applications/Dropbox.app/Contents/Resources/DropboxFolderIcon.icns: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy-lep.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy-lep2.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy2-lep.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy2-lep2.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy2.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy3-lep.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy3-lep2.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy3.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy4-lep.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy4-lep2.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-busy4.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-idle-lep.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-idle.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-logo-lep.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-logo-lep2.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-logo.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-x-lep.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-x-lep2.png: resource modified
/Applications/Dropbox.app/Contents/Resources/dropboxstatus-x.png: resource modified
/Applications/Dropbox.app/Contents/Resources/photos.icns: resource modified
/Applications/Dropbox.app/Contents/Resources/public.icns: resource modified
/Applications/Dropbox.app/Contents/Resources/sandbox.icns: resource modified
/Applications/Dropbox.app/Contents/Resources/shared.icns: resource modified
localhost:~ Username$ 

Since you've manually modified the application, the only solution is to sign the app yourself. (Archived here.) This can also fix poorly implemented auto-updating of applications, though it really should not be necessary.

Warning: Signing the app yourself is telling the operating system to trust it to a very high degree. Don't do that unless you're very sure the application is worthy of that trust.

This happens to me from time to time, especially with iTunes. The issue, as you pointed out, is that the app's signature has become invalid. The easiest way to fix the invalid signature is to reinstall the app.