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How are you transferring the books to your Kindle - are you using "Send to device", or are you just directly copying from calibre's library folders in Windows Explorer?
When you use Send to device (or Save to Disk), calibre will update the metadata internally in that exported copy of the book, which happens to be what the Kindle is interested in for display purposes (not the filename which is irrelevant).
Using a metadata plugboard for the Send to Device case ensures that you have more granular control over the metadata written into the book, such as "fudging" the internal title field to contain series information for sorting purposes when displayed on a Kindle. You didn't say in your original post "why" you were adjusting metadata - I pointed you towards plugboards because if you have the data you want specified in column(s) in calibre then a plugboard is the "proper" way to push that into the file. If however you are just adjusting typos, flipping title/author etc for an ad hoc book and not concerned about series information then it isn't directly relevant.
However if you are just directly looking at the books inside calibre's library folders and directly copying from there, that is the "wrong" way to be doing things quite frankly. For a number of reasons (like being a good way to accidentally screw up your library), but of direct relevance to you is that it is not giving calibre a chance to make those internal metadata updates to the exported books. There are 3 ways using calibre that you can get the metadata updated for the copy of the book that exists inside calibre's folders - to do a conversion as you have done, to use the save to disk feature and then re-import it, or in the case of an ePub to use the Modify ePub plugin.
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