I think civil registration didn't start till the 1850s so perhaps the record never reached the BMDs. I guess JM might be along soon to help with this!
and
There are plenty of events missing from the online indexes. If it was the C of E St James I would bet that the number for the entry is 103/1842 V1842104 26C.
Marriages in the index for St James C of E (groom surname) in 1842 - Church Code CJ:
Missing entry 103/1842 V1842104 26C
I would contact the Registry and ask them about that missing entry.
and I am confident that :
It is very likely that Debra has found the missing reference number, line 103. Back in the 1980s, when the NSW BDM was transferring the details from the manual system to their then computerised system, they did so via the then ‘latest technology’. That technology was the EDP card system. Anyone remember what happened if a card was damaged, jammed, etc? What happened to the data? Well, what if there were apparent duplications? What happened then?
So, from familysearch online there’s a Thomas LEE marrying an Ann WAIT and there’s a Thomas LEE marrying a Mary CLARKE, both marriages are recorded in Church of England parish registers held in Sydney NSW, and both marriages are in January 1842.
I suggest that perhaps at some early stage during the introduction of the EDP system someone may have drawn the conclusion that there was a duplication, and the second card was removed to 'FILE 13".
https://familysearch.org/ark:/61903/1:1:XTCP-VB3 Thomas LEE Mary CLARKE, St Laurence, Sydney. 21 Jan 1842
https://familysearch.org/ark:/61903/1:1:XTCP-Z6N Thomas LEE Ann WAIT, St James, Sydney 27 Jan 1842
Both St Laurence and St James are well known Anglican Churches within the Sydney CBD. The NSW BDM’s Early Church Records for CofE marriages in Sydney Town in 1842 are part of Volume 26C. Both the above marriages should be in that Volume, and the one that is currently displayed at NSWBDM’s online index IS shown as Volume 26C (Thomas LEE and Mary CLARKE is at line 198. (198/1842 V1842198 26C)
St Laurence is Christ Church St Laurence, near to Central Station, Sydney 2000
http://www.ccsl.org.au/ St James is :
http://sjks.org.au/ Quite a number of years ago now, when I was actively transcribing parish registers, I came across a Sydney CBD parish register with several hundred entries that were not showing up on the NSW BDM online index, NOR on the CD/film etc at either NSW State Library or elsewhere.
It took some effort but once NSW BDM was sure that these were extant records, and after the major upgrade to their website, the entries now are part of the online index.
Well sorted Debra !JM
PS when contacting the NSW BDM do not rely on the 'call centre' response. You want a response from the Executive team. Call centre operators can be relied on to mis-understand many aspects of the Early Church Records. I have first hand experience of being TOLD that "V" stands for Vital Records. (It doesn't, it represents the Volume of the ledger compiled in the 1910-1915 era).
http://www.bdm.nsw.gov.au/Pages/about-us/history-of-the-registry.aspx https://www.records.nsw.gov.au/archives/collections-and-research/guides-and-indexes/births-deaths-and-marriages-registers-1787-1856https://www.records.nsw.gov.au/archives/collections-and-research/guides-and-indexes/births-deaths-and-marriages-guide