Could you compare the citation templates from your original and modified output styles files – they should be the same. [Go to the Endnote toolbar, select Edit > Output Styles > Edit (name of the output style file). In the output style dialog box, under the Citations section click “Templates”.]
Also, suggest before switching from one output style to the next, first convert the in-text text citations to temporary citations. then change the output style and click the “Update Citations and Bibliography” option in the Endnote tab on the MS Word toolbar.