Depends, did you edit any of the files or their code? or just install apps/hooks?
Applications/hooks won't be lost, code modifications aka, edits to the files and their code, will be.
Um yes you can upgrade from 3.0.0 to 3.0.1 quite easily, just download the 3.0.1 package and in the documentation folder select starthere.html and click upgrade for instructions.
God I remember IkonBoard....it was quite interesting but IPB was the better product. is iB even still being actively developed? I don't believe it is....
I showed my members and staff clips of the IPB3 test board I have up and they all seem to like it but want to wait for 3.0.1 for the odd bugs in 3.0.0 to be fixed before I perform the update to the boards and blogs system. :)
I'm waiting to update to 3.0.0 because I have a custom modification i want to take with me when I go to 3.0.0. :) Plus the skins I have as well. I'd say it's safe to update to 3.0.1 or even 3.0.2 but i think I'll stay on 2.3.6 just a bit longer. :)
I'm in no hurry for 3.0.0, perfectly fine on 2.3, have a big modification i'm having coded at the moment so i'm probably gonna stay on 2.3 for a good while before going to 3.0.0 even after it goes final. :)