If you are starting again from scratch, i.e. you haven't got any particular mods that you have made then you could just delete the user.config file.
The file will be in your 'C:\Users\xxxxi\AppData\Local\Military_AI_Works' folder where xxxx is your user profile name. In there you will find a folder beginning with 'Matrix.exe_Url'. Mine is Matrix.exe_Url_bponwpd5hjhvh2stp5mhnt5ibbq1etxd. In there you will find folders for config files for each version of Matrix that you have installed.
If you do that you will not have any settings at all so you will have to set up your prefs again, including where you want everything installed to.
Now, as with most things Windows related it is normally advisable to RENAME rather than DELETE so maybe adding a 'SAVED_' prefix to the front of the prefs folder, matrix.exe_url' folder is best.
Then when you run Matrix it will set up again but you can go back if you wanted/needed to.
Now the other thing you can do, if you feel confident, and all you have done is move your previous installation to a new location is to amend the latest user.config file in a text editor.
As before to avoid mishaps you should make a copy of the 'C:\Users\xxxxi\AppData\Local\Military_AI_Works' folder first.
Then drill done into the matrix.exe_url sub-folder and again into the highest sub-folder under there. On my system it is currently, 1.7.1.0 and in there you will find the user.config being used and is in xml format.
The first setting field in mine is:-
setting name="InstallPath" serializeAs="String">
<value>F:\MATRIX\Military AI Works\</value>
What you can do is amend the path to wherever you want the Matrix installation to be installed.
You now have two choices to follow whichever one you follow is up to you whichever you choose you can recover to your current situation by either renaming or restoring the saved folders.
Remember it is always preferable to clean up unnecessary files and folders at the end than wish that you hadn't started something in the first place.
Hope this helps.