Another attempt
Many wait 6 hours after fleishig to eat milk.
So if you finished eating 12:00 PM you don’t eat milk until 6:00 PM
Say you ate meat on 12/31/16 at 11:00 PM You make a mental note that you can eat milk 6 hours later on 1/1/17 at 5:00 AM.
Well wouldn’t you know it an extra second was added at 23:59:60
This means if you want to be exact about it you will be milchigs on 1/1/17 at 4:59:59 which was 6 hours after 12/31/16 11:00:00.
Again it isnt that anything changed with your minhag of waiting, or your start time. Rather it is that the 6 hours that get added have nothing to do with regulatory agencies.
Now imagine there was some halaca that every 6 hours after meat you had to , say pat your head until you eat meat again. So you eat meat at 11:00 PM and now become vegan, you then pat your head at 5:00 AM, 11:00 AM, 5:00 PM, 11:00 PM etc etc.
when you encounter a leap second, that has no bearing on your halachic obligation to pat your head every 6 hours. Only now the time displayed on your clock is different. so you pat your head at 11:00 PM 12/31/16 followed by 4:59:59 AM on 1/1/17 followed by 10:59:59 etc etc. the 6 hours interval doesnt change, the starting point doesnt change, but we disregard an external change made to the clock display (again although it may be accurate) When another leap second gets added. the head tapping will once again shift to 4:59:58.
Again the starting point and interval between taps isnt changing.
Say 27 leap seconds have been added. and you want to tap your head at the exact second required.
You can no longer say well we last ate meat 11:00 PM 12/31/16 so I just keep adding 6 hours and today I tap my head at 5:00 PM. While that is TECHNICALLY true. If you added 27 leap seconds to your clock. when it is next time for you to tap your head it will read 4:59:33. This is an exact multiple of 6 hours after you last ate meat.
The molad is the exact same thing. It isnt based on any actual natural event (though many assume it is, sure the idea is sort of based on an average but as you may know this changes and is no longer accurate at all, and was never accurate on any given month)). It is simply taking a starting point (BaHaRaD) and adding a regular interval 29-12-793 (or 1-12-793) you will get your molad. However much like our head tappping friend., who is doing the exact same thing, To be precise as that molad relates to the time on your clock, you will need to subtract any leap seconds that have been added).
I hope this example helps, if it makes it worse dont get caught up in it