Ok it is not a good idea to use blanks in a table name or a field...
I updated my first answer with a response to this issue.
You will not surround the field name or table name with double quotes but with backticks
splunk_server=ass index="ass_main" host=*pr
| rex field=_raw "(?<EMPID>[0-9]{12})"
| dedup EMPID
| fields EMPID
| stats values(EMPID) as EMPID
| eval EMPID = "'".mvjoin(EMPID, "','")."'"
| map search="| dbxquery query=\"select `Employer Name` PR, `Employee Number` EMPID FROM BIA_BA_EUL.`View Employee Helpdesk` WHERE `Employee Number` in ($EMPID$)\" connection=\"EMP-PR\""
| fields EMPID,PR
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