Reinstalling Flexsync in order to troubleshoot install

I am troubleshoot an issue with our Flexsync reports not opening, we are using out of the box reports.  We have sense upgraded to the Hot Patch 6.1.1.1, however is there a method to do a fresh install of flexsync application?  I have gone back based on the install guide and rerun the application FlexSyncFoundationSetup.exe file, however it shows that it is already installed.  I have also gone back to exported the reports and rerun the sql file that was regenerated.  I know that it is working successfully in our Dev environment which is also on 6.1.1.1.  Would it harm anything by rerunning applyscripts again or would that cause further issues.

Jason,
sorry for the delayed response.  when you upgrade to 6.1.1.1, you need to run the FlexSync Foundation and FlexSync Formulation installers located in EP 3.3, including applyscripts.  If you already have FlexSync installed, this will perform an upgrade for you.
There is an issue with the applyscript that break the translations in the sitemap to display 'no translation found for ...'.  We are correcting this in EP 3.4, but in the meantime, after you run applyscript, you can execute the following query to correct it.
update commonXLAExtensionCacheItem
set fkparent =
     (select pkid from commonXLAExtensionCache where name = 'frmMaster/ctlNavMenu1')
where id in (
     'lblFlexSync'
     ,'lblSingleFormulaPerExp'
     ,'lblFSImport'
     ,'lblProtoExperPerExp'
     ,'lblFormulaExportRpt'
     ,'lblSingleFormulaQtyExp'
     ,'lblFormulaImportRpt'
     ,'lblProtoExperQtyExp'
     ,'lblFSExport'

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