I have been soldering a atmega32u4 to a custom board, before soldering I tested the chip and it was working properly. then I solder it ,uploaded the bootloader again. the programmer says its all fine but the chip no longer show or detect on windows.
Could I have damaged the chip with extra hot when soldering, even when bootloader says it's all fine?
Yes, that is possible; not the full chip probably but certain pins. You can also have a short somewhere (e.g. D- or D+) which provide the USB connectivity.
Yes.
For instance the serial pins could be damadged, which would preventing the bootloader from working.
It's a 32U4 ( ok, 33U4 but I could not find that 
).
I tested every pin with multi-meter and there isn't sorted pins, The bootloader uploads everything as normal. But when connected to the pc it is not recognized, it even appears as an unrecognized device.
Post you schematic! There may be something a new pair of eyes can see.
Maybe so, but a damadged pin might not be detectable with a multimeter.
Of course anything is possible. However when first checking out a new custom board I would first investigate trace mistakes, wrong values, shorts.
You could try uploading a short program to do something like toggle an output or and LED if the board has one. I assume you are using ICP for the bootloader.
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