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Just like any other app, Zotero has its quirks. Here are some and how you might want to deal with them.
This means you have synced attachments that are on different folders. This is eventually unavoidable as you work from different computers with Zotero installation.
Non-solution solution: try to be as consistent as possible with your storage space. A cloud-based storage accessible from all computers with your Zotero installation might work.