Assuming that by "my Kindle" you actually mean the K3 you list as one of your devices, there is no downside that I'm aware of. Save to Disk and a manual transfer via USB has been my almost exclusive method of loading my K3.
That said, loading 2100 books on a K3 is generally a very very bad idea. Too many operations on the K3 become painfully lethargic when it has to deal with a library that large. If you must load that many on the K3 should should do it in modest sized batches (10-40 books) and confirm that it has finished indexing one batch before loading a second. Indexing 40 books, particularly large ones, can take many many hours. Don't expect to load more than one modest sized batch per day.
Though I don't use my old K3 that much these days, I now load only a small number of books (~5-10) from my "waiting to be read" list's "read these soon" sub-list and I delete them when read. My "new" device is a Win10 (nee Win8) tablet and I do the same with the reading app that I use, though I have Calibre with my full library on the tablet as well.
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