Hello,
Before adding/editing files in 12 folder, first take a backup of this folder.
For your issue, You can create new folder in template and add file into it. There will be no impact but make sure that you are not editing existing file (i.e. any default file).
As you said "non-standard solution to deploy solutions", if it is some custom package like wsp then you can deploy this WSP package to other server without doing any manual work.
Hope it could help
Hemendra: "Yesterday is just a memory,Tomorrow we may never see"
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