Holmes and Flanagan will officially be reunited at St George Illawarra training on Monday, when the Dragons recruit officially begins his pre-season in Wollongong.
The star centre's move to the Dragons was a key signing for Flanagan, offering much-needed strike and goal kicking to replace Zac Lomax.
Flanagan personally flew to Townsville to meet with Holmes and his wife in August, once it emerged North Queensland were willing to release the 29-year-old.
But it is not lost on Holmes how different things are with Flanagan this time around.
He won a premiership under Flanagan at Cronulla in his second full season in the NRL and was identified as the Sharks' long-term fullback.
But he stunned Cronulla when he walked out on the club at the end of 2018 to move to the US, with a year still to run on his contract and a five-year deal on the table.
Cronulla captain Paul Gallen was openly critical of Holmes's exit and called for the NRL to ban him from returning, a statement Flanagan supported as he publicly admitted his own frustration.
"I was young and naive and felt like I could do anything at that time," Holmes said.
"I wanted to test myself somewhere else. Not many people would do it, they might go to another team or go to rugby or something like that.
"The opportunity arose for me and I just wanted to take it. Whether it was good or bad for me, I still learned from it and came back a different player.
Dragons head coach Shane Flanagan flew to Townsville to get his man which impressed Holmes. (Mark Evans/AAP PHOTOS)
"I don't think I told (Flanagan) personally (that I was leaving), maybe my manager did. I would have been 23 or 24, probably too scared to talk to him."
Flanagan and Holmes eventually did clear the air before the US trip, but had limited contact after that.
But Holmes said he had been impressed with the fact Flanagan had flown to Townsville to meet him, and feels far more at ease with the coach now.
"Once (the Cowboys) gave me permission to talk he reached out to my management straight away and then flew up, met with my family," Holmes said.
"That was pretty good from him. I don't think many coaches would do that. It showed how keen and interested he was to get us down here.
"He's been really supportive (since the move down), every time I have gone to him.
"When I was a bit younger he would probably have been a bit harder to talk to. But now I am a bit more experienced and a bit older, I find it a bit more comfortable."
Holmes is still recovering from a broken lower leg suffered in North Queensland's NRL finals loss, but is expected to be fit to start the season.
