When first reading your post, I didn't understand your intention because of the reported "Can't recognize silicon ID", which isn't directly related to the "Using POF for indirect JTAG programming" question in my opinion. Unfortunately you didn't explain about "I need to use a POF".
Basically, a *.pof file created for direct EPCS programming and the respective *.jic file are identical except for a few header data. They can be converted into each other, but the Quartus Programming File Conversion tool hasn't the option. I guess, it wasn't intended as necessary action in the regular design process. But you can e.g. program a *.pof file to an EPCS device through AS programming and read it back as *.jic through indirect JTAG and vice versa. You have this as a last resort.
Regarding the said "Can't recognize silicon ID" problem, we should know the condition in detail. Generally, if you don't manage to include the SFL in your design, you should start with the factory default SFL design shipped with Quartus. It should always work, if the EPCS hardware is functional. Before Quartus 9, SFL couldn't coexist with other virtual JTAG instances in a design, e.g. Signaltap or Source&Probe due to a Quartus Programmer bug. The issue has been discussed in the forum before, but it's solved now.