You need drivers to activate the second port, so if they fits you could put them on the emergency disk, or put the cd rom on the first port as slave (and adopt the dosdriver for your cdrom to suit your new config).
I know, but I don't know how to do it

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I can't connect CD ROM to first port as a slave, since I want emergency disk that will "rescue my Amiga" without switching ports.
I moved FastATA drivers and preference to floppy, edited startup-sequence, put CD2 into DEVS: but there is still no CD ROM detected when I boot from Emergency-Disc

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Can someone help me with more detailed instructions?
Thank you!