Autoloader File Resolution Issues

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Hello,
We're working on migrating a large number of files from a network structure to Vault 2017. The folder structure is basically isolated project files with our main assemblies, one folder with our custom created library parts, and one folder with commonly used parts, all on a network location. In order to speed the process, we're attempting to copy our network directory files to our local drives before running autoloader. All files in the main folders and commonly used parts folders resolve fine, but the library files still point to the network, resulting in file not found errors. Is this a common problem and does anyone know if there is a fix or workaround for it? Currently we need to set up our single user project file with a search path to the network for the library parts, and it is resulting in excessively long processing times for autoloader.
On a related note, when autoloader finished scanning and going through the mapping process, we often run into an error during the file validation process (we've been unable to get an answer on what this "validation" is actually doing). At that point autoloader exits and we're left back at square one with no real direction on how to fix this file validation error.
Thanks in advance for any advice you can offer.