FTP and interacting with your server would be a hosting based question. Your hosting provider would be able to instruct you on how to connect to your server using FTP and upload files correctly to the folder you want.
Unfortunately, we cannot control the whole process or when things go wrong. Being a self-hosted customer, there are steps in between which you may need to manage in the event there is a software or server issue. Typically, when there is an issue with the files extracting, this is an issue with permissions or otherwise on the server so once you are up and running you may wish to having your hosting provider review your server error logs so that your next upgrade does not encounter that.
Alternatively, if you are not comfortable managing your server, like you would on a self-hosted installation, we do have our Cloud which is fully managed by our team and because we control the infrastructure, obtaining files/etc... is easier as it is done completely different than through technology that self-hosted servers require. Thus there is less room for error and if there ever is an issue, we are both your software and hosting support so can help you very quickly resolve any issues. You can read more here: https://invisioncommunity.com/buy
If you would like to supply us with FTP access, we can take a courtesy look at the extraction though to see if this is something in the software causing this. If it is on the server, we can provide next steps for your hosting team to take over. To do so, please add access per the below:
We would need to look further into this for you, however the access details on file appear to be incorrect or missing. Could you please update these details by visiting your client area, selecting the relevant purchase, then clicking "Review/Update Access Information" under the "Stored Access Information" section.
We look forward to further assisting you.