If you need to migrate all data from one seeddms installation to another then just copy the data folder and dump/import the database.
Do you really need this tools? Which database are you using? Are you planing to change it?
6.0.39 already includes the changes.
I once started an extension called 'internal link' which is similar to a symlink in a file system. It was never finished because of lots of small problems, like access rights, notifications, etc.
I already did some changes which may partly solve the problem. The problem is basically that seeddms tried to create the preview while generating the list of documents within a folder. If a single preview generation fails, the whole list isn't shown. I removed that part and delegate the preview generation to op/op.Preview.php. Now, if a preview cannot be created, the list of documents will still be created, but that single preview image will be missing.
The extensions are located in www/ext. The extension manager can be opened in SeedDMS in the admin are.
The pdf viewer has been moved into an extension which is shipped with 6.0.38. Did you activate it in the extension manager?
I guess SeedDMS is trying to create a preview of that large image and fails. Unfortunately, this prevents the listing of the folder where that document is located. There is currently no quick fix, but turning the creation of preview images off by taking out the line which adds the conversion service in inc/inc.ConversionInit.php. Are you familiar with PHP? How large is that picture?