Well assuming that TNA have located your father's records, all should be OK. I seem to recall that your father was Pte Godderidge 11400830, and TNA certainly should have his records, rather than the MOD. However my understanding was that the MOD had retained their indexes to the records which they had transferred to TNA, so it is somewhat surprising if they say they can't identify where your father's record is.
This situation is at the heart of why it is taking TNA so long to re-index and catalogue the MOD Files. It may help if I outline the old MOD system. Prior to 1996 each of the larger Corps (eg the Royal Engineers or Royal Artillery) and groups of Infantry Regiments had their own Manning and Record Offices, which were dotted all over the country. Each maintained their own soldiers' careers and documentation and the 'central staffs' (as they are referred to) had no direct knowledge about individual soldiers. The Army Personnel Centre in Kentigern House in Glasgow was created to bring all these separate outlying offices together in one building - and in the process lost most of the old staff who weren't prepared to move to Glasgow from places like Exeter or Brighton.
But even within the new APC structure, the separate Corps and Infantry Divisions maintained their own sections, with just the administrative support being shared. Individual clerks would know a great deal about the soldiers they looked after, even though they had never met them. Once a soldier left the Army his record would be archived but kept close at hand, in case there were matters concerning his later life (eg pensions but also welfare cases). In almost all case the MOD will have recorded when a soldier died even if this was decades after he had left. As you can imagine although standard forms and procedures were used to document a soldier, his actual file could be a mishmash of different pieces of paper. In theory digitisation was suppoed to reduce the amount of paper, but even so a personal file would still be held in paper form (as I believe it still is today) alongside any digital records. Obviously the soldier's Army number was the key identifier, but for day to day management purposes it is the trade and rank of the individual which matters. So to take an example of a Royal Engineer, a combat Engineer Lance Corporal's career would be dealt with by a separate section to the one dealing with Electrician Sergeants.
As the time arrived to transfer the older (pre 1969) files to TNA, they had to be dug out from their various repositories, palletted up and sent off to Kew accompanied by a sort of manifest showing the contents of each pallet. Due to the age of the documents concerned, covering the period from 1920 to 1969, the records were in a number of formats. For example true Army-wide numbering was not introduced until 1950. Prior to that date numbers were issued in blocks to the various regiments and corps to allocate as they saw fit. This meant that there were many unallocated numbers. After 1950 the numbers were issued to an individual centrally based on when he enlisted and there were no gaps in the numbers issued.
The staff at Kew had no intimate knowledge of the various systems of indexing used by the MOD and before 1964, the War Office. Hence they started with the first pallet of documents and painstaking went through the files and re indexed them, extracting the information they required for the Discovery database. That is why some of the earliest files to be processed were a relatively small batch of 56,000 REME soldiers which can be found in WO 420. REME was not formed until 1943 and so the time period concerned was much shorter than dealing with files going back to 1920.
If you have 13 minutes to spare, this video produced by TNA explains the work behind the cataloguing process:
https://www.youtube.com/watch?v=wpCgYrp19Bc
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