According to: SharePoint v3 Localized Resources
If the assembly is deployed to the GAC, then the folder structure
containing the web parts resources will be in the virtual wpresources
folder and the folders will be named as follows:
folder is physically located in this global location: C:\Program
Files\Common Files\Microsoft Shared\web server extensions\wpresources
If the web part assembly is deployed to the Web Application’s bin
folder, then the web part’s resources will be in the physical
wpresources folder (no underscore) in a sub-folder named after the
So if you have single solution deployed on multiple web applications you need to put your assemblies into Web Application BIN (it makes sense). GAC vs BIN is always about permissions (didn't find any articles on using resources).
Alternatively you can always re-deploy solution on some other web application an you will have your resources back.