Duplicate folders created in working folder for GET functions in Vault

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My company has been using Vault since 2013. We currently use Vault Pro 2017 and will soon be updating to Vault Pro 2019. When Vault was first started, I wasn't with the company and they added all of the files using auto-loader and had no structure or sense to their paths, plus they had numerous duplicate files.
I have done what I can to restructure Vault into a cohesive and workable format, i.e. getting rid of a lot of the duplication and correcting and organizing the folders and path files. When I started they were using new ipj's per job (174 different ipj's) and now we use one common ipj for every job, but we've come across a problem.
When we check out through Inventor or the Vault Add-On in Inventor it creates the correct file path and folders, but when we use the Get function in Vault it creates a duplicate folder inside of the working folder on the hard-drive. (See photo)
We need the Get function to go back to previous versions, but like I stated earlier it creates duplicate folders, so then we have to manually move the file into the correct folders and file path on our hard-drives, that it would be in if we had checked it out through Inventor or the Vault Add-On in Inventor. This can get crazy really fast, not to mention it can cause issues on the check in, do to the name already being used in that folder in Vault.
My question is, how do I fix this problem so that when the Get function in Vault is used it puts the file in the correct location on the hard-drive, whether it is a previous version or the newest version? I was wondering if it would be a good idea when we update to the 2019 version if we started from scratch in a way, put all the files on an external hard-drive, then install a new Vault with all new Working Folder and path structure. Then start checking files in, while getting rid of duplicates at the same time. Is this a good way of fixing the problem?
Before you respond with sending me a link to this page, Using Autodesk Vault with a Single Inventor Project, just know that this is what I used as a guide to implement the change to using a single ipj from the 174 that I started with, the only step I didn't use is the very first one because, 1. I don't have access to the ADMS Console, 2. We already had a working Vault (i.e. I wasn't starting from scratch). But I have enforced both the Working Folder and the single ipj.
Just in case this makes a difference, we work off of one Vault but two servers in two different locations/states, we use the replication method. We have recently been having the problem of files disappearing if one of the sites looses power. Could this be a related issue, or something completely different? Any help would be useful, sorry for the long post.