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One problem with uploading files in a Shiny application that has multiple sub-applications is that the uploaded files may not be accessible or usable by other sub-applications. Each sub-application in a Shiny application operates independently, with its own server and user interface, and may not be able to access files uploaded in another sub-application. This can make it difficult to share data or files across the entire Shiny application. To overcome this issue, one possible solution is to store the files in a shared location, such as a database or file system, that all sub-applications can access.