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Theoretically, you shouldn't be seeing the file names of the log in the vault browser if you have embedded them in your template.
If you have used linked image image files, they should show under a 3rd Party group in the vault browser. (Which in your case, the 3rd Party group is missing)
Would it be possible for you to upload your template file and logo to this thread? We can do further investigation from there.
I checked your template file and it seems to have a number of unreferenced XREFs attached to it.
I have detached these XREFs and your template (see attachment) should be free of them now.
Let me know if this works for you.
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