Export the glossary > this will give you a xml file which contains all the entries in your glossary. get a good text editor (not word. I suggest you look at "vim" or "jedit") and do a search and replace on <USEDYNALINK>0</USEDYNALINK> replace it with <USEDYNALINK>1</USEDYNALINK>
You should replace this for all entries you want to auto-link.
In case you want to make the entry-linking case-sensitive you need to edit <CASESENSITIVE>0</CASESENSITIVE> to <CASESENSITIVE>1</CASESENSITIVE>. To match full words only edit <FULLMATCH>0</FULLMATCH> to <FULLMATCH>1</FULLMATCH>
Then delete your glossary and recreate it (or delete the specific entries one by one) and import this XML file back into the glossary.
Hope this helps.
Riaan