How about something like this (untested):

<cfset crlf = chr(13) & chr(10) />
<cfset lineArray = reMatch(crlf, myFile) />

<cfif len(trim(lineArray[26]))>
<cfset invoiceNumber = trim(lineArray[26]) />
<cfelse>
<cfset invoiceNumber = trim(lineArray[27]) />
</cfif>

The variable 'invoiceNumber' should now hold whichever line has content ... 

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