You will need to request a new certificate. The Default Certificate will contain the names of Lync specific hosts (pool, meeting URLs, autodiscover, etc) within its Subject Name and SANs, where as the OAuth certificate is just the domain name as it's Subject
Name.
You will probably also find that when you created the Default Certificate it was marked as not exportable (unless you explicitly changed it on request) - the OAuth certificate will by default be marked as exportable as it will replicate to other hosts as
required.
Regarding the Share Permissions, check out Jeff Schertz's article on the permissions required here: http://blog.schertz.name/2013/03/breaking-down-lync-file-share/
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