> Is there any elegant way to do so
Not really, assuming your GUI isn't the cause of the problem.
Some operating systems and programs that open the file can be set to avoid opening duplicates but Matlab does not have any control of that that I know of. Furthremore, even if you use a counter or store a list of documents that were accessed, the matlab program wouldn't know if the user manually closed those files.
If your GUI is listing duplicate files to open within the same command, that could be easily fixed, of course (unique()). Example:
docs = {'myfile0.pdf', 'myfile1.pdf', 'myfile1.pdf', 'myfile2.pdf'};
% [^ duplicate]
for i = 1:numel(docs)
winopen(docs{i};)
end
