I also tried naming the file art%253A10.1007%252FBF01034471.pdf as the OP had 
done.
I can ls -l the file and open it as well.
Both documents were created by right clicking and creating a new document and 
renaming the file to have a % in the file name. Second file was also created as 
a pdf from LibreOffice and still worked properly. The problem may be specific 
to the file you have or your installation of Ubuntu. Can you give more 
information to help us issolate your particular problem?

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to evince in Ubuntu.
https://bugs.launchpad.net/bugs/1112641

Title:
  Evince incorrectly reports document Location in its Properties if
  there are % in filename

Status in “evince” package in Ubuntu:
  New

Bug description:
  I have a file named 
  art%3A10.1007%2FBF01034471.pdf,
  if I open document Properties (Alt+Return) for it I get
  Location: 
file:///home/username/Documents/PDFs/art%253A10.1007%252FBF01034471.pdf.

  So there are extra escape sequences for percent sign (I know that %25 is a 
code for %). If I try to 
  ls -l /home/username/Documents/PDFs/art%253A10.1007%252FBF01034471.pdf I got 
ls: cannot access 
/home/username/Documents/PDFs/art%253A10.1007%252FBF01034471.pdf: No such file 
or directory.
  If i try to navigate to correct file 
/home/username/Documents/PDFs/art%3A10.1007%2FBF01034471.pdf I get no error.

  So there is an error in % sign processing in evince.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: evince 3.4.0-0ubuntu1.4
  ProcVersionSignature: Ubuntu 3.2.0-36.57-generic 3.2.35
  Uname: Linux 3.2.0-36-generic x86_64
  NonfreeKernelModules: nvidia
  ApportVersion: 2.0.1-0ubuntu17.1
  Architecture: amd64
  CheckboxSubmission: a3c9de473bf7a483a92609c6b20d2aee
  CheckboxSystem: b633b4f40868d491c2ae5b50030ce6f3
  Date: Fri Feb  1 20:15:58 2013
  InstallationMedia: Ubuntu 10.04 LTS "Lucid Lynx" - Release amd64 (20100429)
  MarkForUpload: True
  ProcEnviron:
   LANGUAGE=en_US:en
   TERM=xterm
   PATH=(custom, no user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: evince
  UpgradeStatus: Upgraded to precise on 2012-09-28 (126 days ago)

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