firstly the 3000 kms oil change interval is actually harmful for your engine. Engine oil - specially gp3 and 4 blends have excellent HD additive packs in them which are thermally activated.
when you install fresh oil the high level of detergents get to work in cleaning off the old patina from the engine and deposits it on the filter - after the detergent has worn out the oil then starts to deposit the anti wear metals or solid lubricants to engine parts which provide the long life coating.
this total cycle in a small sized engine sump with a not much stressed modern design engine takes about 10,000 kms (urban + highway) - If you are overly paranoid about "dus hazaar kilomeetur oil change" - then replace the oil filter at 5000 with adding a cup of new oil.
Its also normal for it to reduce a slight amount of oil between oil changes too.
you are overcleaning your engine which is known to cause high level of wear - 3000 kms oil change is acceptable for engines like the old VW beetle running on API SC oil.
btw - I saw you wrote silicone to seal engine sump - what silicone was this? bathroom grade RTV? or actual engine sealant?