The files on the server are compared with the original data (to ensure completeness), but if a difference is detected, the resulting files may be unavailable. If a folder upload includes files that are modified by the operating system (i.e. 'Thumbs.db', 'desktop.ini') then you are increasing the chances of the file being modified after the uploaded starts. 

To minimise the chance of issues;

Ensure you use a wired (Ethernet) connection in preference to Wi-Fi.
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Save and close any files that you intend to share, prior to upload (especially important if uploading from a shared area).

Exclude any system files that are not specifically required in the upload.

Do not move files or folders in Windows Explorer whilst the upload is taking place.

Do not rename any files or folders whilst the upload is taking place.

If the data is on a network drive and very large, it will be faster / more stable if you copy the data to a local drive (i.e. C:\Temp). This means you can also switch off any VPN that you would need to copy files.
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​Uploading a folder with more than 1,000 files?

Web browsers cannot track uploads of 1,000 files or more, but if you compress the data first and upload this compressed data then the problem goes away. If the files includes special characters, use 7zip to preserve the filenames. The contents of the compressed file will be recorded within MX.
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