It is unlikely that the waveguide itself is damaged beyond useful repair. Waveguide is nothing more than precision pipes. Often bad waveguide is replaced instead of repaired. If the internal cavities were exposed to smoke damage then careful internal cleaning to get any soot out of the cavity before it can be possibly reused. Once the waveguide path ways have been reconfigured there maybe a need to perform the RF black magic of dent tuning the waveguide.
Much more critical is when the waveguide was damaged, it could have taken out many very expensive, long lead time components:
Power amplifiers (traveling wave or klystron tube amplifiers)
Low noise amplifier
Magic T
RF power isolator
Waveguide filters (both pass and time equalising)
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"Don't disturb my circles." translation of Archimedes last words
I used to be around some rather interesting characters. One of them claimed to have done 120 GHz work before 120 GHz existed (wink). He claimed that he was provided with a huge tool box that was nothing more than calibrated ball bearings, calibrated magnets and a very wide assortment of calibrated hammers. He claimed he would tune up a system by dropping in a ball bearing and moving it around with a magnet on the outside of the wave guide tube. Based upon his knowledge of black magic he would then decide to either leave it in place, roll it out and replace it with a different size ball bearing or use a precision hammer to make a precision dent. He might do this for days before he was happy.
I suspect that everything was machined down to the thousandth's of an inch. Using a hammer to make the system work properly seemed so silly that it probably was true.
All this was done while wearing a pointed purple hat with big white dots on it. They wouldn't let him wave his wand around or sprinkle pixie dust.
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Few things limit our potential as much as knowing answers and setting aside questions.
What is involved in repairing damage to waveguides?
Bringing them back to nominal print dimensions and performance qualifiers.
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If you want to know how well a broom works you do not ask the guy selling the broom or the guy who designed the broom, you ask the guy using the broom.
We are talking FAA here, it is very unlikely they used anything much above 20 - 25 ghz, likely much lower....what i would do is check the S-parameters before and after the repair, and decide if the degradation in performance due to the repair is acceptable compared to the cost of replacement.
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