I replaced all of the caps, I also replaced the Audio RCA connectors as well. Everything works perfectly, but I noticed an issue where the filter is always enabled on the right channel regardless of it being switched on or not (left channel still works as it should).
The filter circuit is simple enough. Essentially switching it on/off puts either +12V or -12V on the gate terminal of both JFETs Q321 and Q331. When the JFET is turned 'on', then audio bypasses the low pass filter formed by C332, C333, R332, R333. See page 6 of the schematic:
http://amiga.serveftp.net/Schematics/A600_schematics/A600_R1-5_schematic.pdfI'd suggest starting by confirming that you see +12V/-12V on the gate terminals of both JFETs when the filter is switched on/off.
https://www.amigapcb.org/ is useful to locate the parts and correct terminals. If you're not seeing the +12V/-12V on one of the JFETs, then work backwards from there, you may find an open circuit track caused by corrosion damage.
If you are seeing +12V/-12V on the gate terminals, the right channel JFET (Q331) might be bad. Replace it with the original MPF102, or a commonly available BFJ310 will work equally as well.
The left/right audio circuits are identical, so you can directly compare readings between them. Amiga Test Kit has a handy function of generating a 10kHz tone to test the 4kHz low pass filter, and you can easily toggle the filter on and off.
I have looked at the rev 1.5 schematic and read somewhere that removing C331/C321 on the underside should bypass the filter but in this case doesn't seem to make any difference.
WTF, where did you read that garbage? C331/C321 forms part of a fixed 27kHz low pass filter (by my calculation), and isn't part of the audio switch.
If you never want the 4kHz low pass filter to be enabled, and don't care about aliasing artefacts, then you can effectively disable the filter in multiple ways. For example, linking the source and drain terminals of both JFETs would do this. Or connect op-amp pins 5 to 8, and pins 3 to 14. Or remove C322, C323, C332, C333.
Hope that helps.