You don't want to copy any files directly to the sync target,
Joplin works a bit differently than obsidian where it's not looking at a vault of files directly on your filesystem
Joplin stores your notes in a sqlite database. Any attachments are stored in a folder under your joplin profile directory, but joplin keeps track of them in the database (each resource has a resource id, e.g. :/f95fc3ed93c0437ebe47c513cdc906aa). The files that you see on onedrive are a copy of your notes/attachments used only for synchronization.
To add attachments to joplin, you would drag and drop the file into a note or use the attach file button in the note toolbar and joplin will handle adding the attachment to the database/resources folder.
If you're importing notes from Obsidian to Joplin for the first time, you can use the built in markdown import (file | import | markdown directory) which should handle importing attachments and directory structure.
The key thing before doing the import is to make sure that your obsidian links are using standard markdown link format, e.g. for an image:
not wikilinks format, e.g:
![[filename.jpg]]
If your obsidian attachments are currently using wikilinks format, a few options to convert them:
GitHub - bingryan/obsidian-markdown-export-plugin: This plugin allows to export directory/single markdown to a folder. support output format(html/markdown/text) - enable the "Convert WikiLinks to Markdown" option
GitHub - ozntel/obsidian-link-converter: Obsidian Plugin to scan all your links in your vault and convert them to your desired format. - however, IIRC I had some significant issues when trying to use this one where it mangled http(s) hyperlinks and any links containing parentheses. Highly recommend backing up your vault first if you try this one 
Jimmy: https://discourse.joplinapp.org/t/jimmy-a-joplin-import-tool