Baxter took issue with Strasbourg's apparent vague notification and delay in submitting proof that their new signing Mothiba is injured.
The frustrated Brit on Monday threatened to report the Ligue One club to FIFA over the matter, but has since softened his stance with a view to future dealings with the French side.
Baxter called up Bidvest Wits attacker Mxolisi Macuphu the following day as a replacement for Mothiba ahead of Saturday's African Nations Cup qualifier with Libya at Moses Mabhida Stadium (15h00).
"No. I mean, look, you talk about Lebo Mothiba's team; we got an email from them saying that they objected to the complaints that we made," said Baxter when asked if he is pursuing the Mothiba matter with FIFA.
"But the truth is, we had Amiens [Bongani Zungu's club] calling us, mailing us during the game about Bongani Zungu's injury and we get a letter directly from the doctor.
"[With Strasbourg] we had to wait three days before we got the doctor's [letter] and Lebo was not here. We only had one contact from the club secretary saying, 'Lebo couldn't come here because he had a physical problem'. We didn't know what that problem was, three days later we got the scan.
"I'm questioning they way that was done and they are questioning possibly what we did. But I think, in terms of going forward, we need to have relationships with every club.
"We ought to be given respect in that we are trying to do a job here. Not just they bought a player with a lot of money and he's their property, no, he's not.
"He's our player as well and we need to do a job here. We need information about our players as quickly as possibly, as soon as they are injured. We are trying to get that with South African clubs. Amiens, they did that and some others do that.
"So we are getting there, but this is a new relationship with Strasbourg ... I don't know the people there. But I just know that we need to have immediate information about players, open and honest information. And then there's no problem."