Hi @AndreVB ,
About 1): I don't see (at least with my IDE 11.4.1) the the LinkServer connection is erasing first all memory. I do have in many projects reserved a region at the end of the flash. But I simply reduce the flash size in the MCU settings:

I can confirm that way for all debug connections I use (Segger J-Link, LinkServer McuLink & P&E Multilink) the FLASH that way does not get touched, showing with MinINI and McuFlash below (from https://mcuoneclipse.com/2021/12/19/key-value-pairs-in-flash-memory-file-system-less-minini/ )

Maybe the thing you see is because you are using an older IDE? I remember (I think it was starting with 11.4) the LinkServer flashing has been optimized, not programming untouched sectors by default (something what J-Link always did, and P&E does now too, at least when I last checked). You could verify the flash operations in the Console view:

About 2): on the KL25Z there are the FPROTx registers which can be used to protect each of the 32 regions of the flash memory (see chapter 27.4.1 Flash Protection) in the KL25Z reference manual.
I hope this helps,
Erich