I was surprised that Gold Wings say to check oil hot, right after motor is turned off. With most other bikes I have owned they say to wait at least 20 min after turning off motor before checking. (never understood this as most had oil tank higher than motor, so nothing more will drain into tank) With the HDs and my Yamaha I just fill tank full as you cannot overfill. (except for expansion)
I never trust a site glass. (I have had site glasses get a bubble or airlock and look full but be empty, I had this problem with hydrolic clutch on mt truck before)
Also be careful with dipsticks. Some bikes say to pull wipe and just set back (not screw in) in to check, others say to screw dipstick all the way back in before checking. Also most bikes are marked at one quart (US) low, however some will be marked at one quart (UK) or at one litre, some are marked at one pint (UK)
AS to the OP
I have had several things turn up missing from my panniers before (Gloves, coat, tools even groceries all in Pueblo,CO several times) Also had a coil and plug wires disappear from a Harley (again in the high crime city of Pueblo, this was at Safeway)