As TilVl said the JTAG portion stays in place...That is the wiring connected to J2D2 with the diodes connected to it. The NAND portion be it pin headers or QSBs or wires soldered directly to the board can be removed if you wish to keep and re-use them but since you're rather new to soldering I suggest leaving them in place as replacements can be bought for rather cheap if you ever run into another JTAG. Just my .02 by the way congrats on your first successful JTAG.
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