If you download the following pdf [1], you will notice blue underlined hyperlinks in the references section (last page). Can these links be removed together with the light blue underlines? If yes, how? If not, why?
Also, the pdf contains other hyperlinks for bibliographics references (like [46]) or equation numbers (like (9)) in plain blue. Can this plain blue be tranfor;ed into plain black? If yes, how?
No, the blue underlines are created by ResearchGate for sure (I do not know how exactly). Essentially, authors upload their pdf files, then ResearchGate has a look at its database to see which cited bibliographic references are already available in the database, and then create links. What I find strange is that these links do not seem to be removable easily in Acrobat Pro.
It does not matter which application created these underlines, but you may want to think twice before trying to argue with TSN 
What's important is that the underlines are graphics content that is independent of the link, so even when you remove the link, that line remains in the PDF file. There are ways to identify these elements, and then remove them, but that would require a custom Preflight fixup, in which you describe exactly what you want to remove (e.g. in your case "is line", RGB value of [0.333, 0.694, 0.961], line with of 1.0pt). You can then run this fixup, and it will remove all lines that look like your blue underline. I just did a quick check, and it identified 68 instances of such lines in your document.
Keep in mind that this will also remove any blue line that matches that description, but is not a line under a link.
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