Each time he lost time, there has been a definable reason for it, which does not necessarily have an impact on the rest of the race. He lost 11 seconds in the first hilly stage. There was in initial attack by Landa, Bernal reacted there was a gap and once the gap was established, Remco did not keep losing time. He has never been a punchy rider, and especially now with a short preperation and training, there was no more time to train his short efforts.
First MTF he did not lose time to Bernal, only boniseconds. Same problem here, he was outsprinted. It's not his thing.
Two days ago he lost time on the final gravel section. He was badly positioned and again he does lack the punch that Bernal has.
Today he was wasting energy due to a lack of technical and bikehandling skills on the gravel sections. You can make up for that, closing gap after gap, moving to the front again after every turn and corner, but you have to do a lot bigger efforts than your rivals and at a certain point you run out of energy. Also, after being dropped and Bernal going all out, he only lost 2 minutes, caught Bardet & Martinez, and nearly Soler and Ciccone. He he really been done and dusted, i don't think he would have been able to lose so little time.
While it's completely possible that he'll drop further back, due to a too short training period, the time he lost does not necessarily point to that being the case. There are enough reasonable explanations for each time he has lost time.
Who knows, but as Bonimenier said, according to the team, there were technical issues with communication. It's a flimsy excuse honestly, since he (Almeida) shouldn't need to be told to begin with, that he should look after Evenepoel, but on the other hand, he did do a lot of work once he went to help.
But i agree about Remco, it's not the end of the world, only a minute off podium. He didn't completely tank either, even caught guys from the first group. If he can bounce back, still a lot is possible. The main question is, were these the signs that he's running on fumes, or is nothing the matter and was it a bad day due to woeful bikehandling, making him burn through his energy reserves.
Had he started helping earlier, Remco would not have lost so much time in the first place. Both of them would have wasted less time and energy, and possibly even been able to (perhaps temporarilly) bridge the gap.