Answer is YES! I went through that path some months back and all was well. You need to delete or rename the WIN.COM file in C:\Windows folder from DOS. Make sure your boot floppy has the drivers etc to allow access to your CD Rom drive. Then just run SETUP.EXE from your full version of Win 98SE.
I must add that it is always better to do a "Clean install" of a new operating system, BUT doing it as above certainly shortens the time taken and the subsequent hassles of reinstalling programs.
Good luck
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