First off WELCOME to the forum.
I can almost assure you the helicopter pilot had no clue you were flying in that area what-so-ever. Being able to spot a small UAS (I'm assuming you were flying an
Air2S or similar) on the horizon is hard but spotting one below the horizon is going to be a very difficult task.
I want to caution you about "holding position" because you need to keep in mind if you had a Loss of Signal for some reason your UAS is probably going to ASCEND and that's the HOT ZONE! I am a firm believer if there is an aircraft in your vicinity and it's even possible on a similar flight level than your UAS, you land and you land immediately. There is no reason to even chance a RTH putting your aircraft in line with the manned aircraft.
I had to do exactly that this last Saturday when mapping for a client. I was flying at 300' AGL doing an autonomous Grid Flight over 99 acres of a tree farm. My VO picked up on the "sound" of another aircraft in the area and she alerted me. I immediately put my finger on the "Mission Kill Switch" (mode change switch) and waited for her to visually locate the source of the sound. In a few seconds she pointed it out and it was a Military C-130 (assumed) flying through at roughly 700'AGL (
we are in a MOA so seeing low Military aircraft isn't unusual at all). I don't know if you've seen a huge plane like that down low but it's freaking HUGE! I immediately changed mode to stop the autonomous flight and made a bee-line for our landing area. The aircraft was here and GONE before I made it back to me but I was doing anything and everything to minimize risks... both of a air incident and also of loss-of-signal etc. Even though my RTH height is set WELL below my "Guestimated" altitude of the manned aircraft my SOP is to get it DOWN and get it CLOSE to me ASAP.
Be warned that it's common for General Aviation to fly (legally so) below 500' AGL and ALWAYS keep your head on a swivel and not solely relying on Aps etc. Keep a solid VLOS and utilize your "Mk-1 eyeball" always.