two in-text citations when combined, one is proper and other remains with curly brackets even after updating bibliography and CWYR turned on

Those characters?  Where do they come from?  They shouldn't be there.  Inspect your records for any random or if you edited the citation and added any stray characters in prefix, suffix or cited pages boxes.  Remove that extra internal { and any ` charachters which should fix it.  If it doesn’t fix it, then come back, as the error must be in how endnote enters the temporary citations or in the output style itself.  so, also attach the output style you are using. 

They should look like this {Freeman, 2010 #512; Dent, 2000 #602; Dent, 2000 #602}.  which should resolve to (Freeman et al, 2010; Dent, 2000) or something similar (duplicate should not show).  The ` tells endnote to treat the following as true text and not to be interpreted by endnote as a special character.