I've found articles that talk about attempts to set up a Single Pro-Remain candidate to stand directly against the Brexit party. The linked article makes clear these talks broke down, but doesn't explain why Change UK decided to not stand at all while each of the other Pro-Remain parties did put forward their own candidate.
There are two plausible explanations, the first being that they didn't want to contribute to further splitting the Remain-voting bloc, and the other being that they couldn't find a candidate in time.
To provide context to the situation alluded to in the question; originally the main Remain-supporting parties, the Greens, the Lib Dems, Renew, and Change UK had all planned to stand down their individual candidates and back an independent, pro-Remain candidate. This was decided on Tuesday the 7th of May, two days before the deadline to register candidates, to be Femi Oluwole.
After wrestling with the decision on whether or not to stand for two days, Oluwole eventually decided not to run on the morning of the deadline. The reasons he gave for his refusal were fear of splitting the remain vote, handing victory to the Brexit party, lack of local ties to the area, inability to dedicate enough resources to the by-election while also working on the European elections, and ethical reasons related to his involvement in the Our Future Our Choice campaign which he co-founded. Oluwole threw his support behind the Labour candidate, who had not been involved with the talks to run a unity candidate, and indeed, as the link in the OP says, "made it clear that they would strenuously disrupt the campaign and obstruct an independent candidate".
Faced with less than 24 hours to choose candidates to run before the May 9th deadline, it seems that Change UK either failed to find a candidate willing to stand for the party, or decided that running another pro-Remain candidate would help hand victory to the Brexit party by taking votes from the Labour candidate. Given that the candidate that they ended up supporting in the by-election, Renew's Peter Ward, eventually won just 45 votes, it seems likely that the party had found that their level of local support was negligible, and therefore that running a candidate would be wasteful, given the upcoming European elections. It is also possible, given that in April, Renew announced that they would support Change UK in the European elections, that there was some sort of private deal between the parties to trade support and pool resources.
In conclusion, then, it seems that while there is a lack of clarity surrounding this decision, and certainly no official explanation of their decision-making process besides wanting to avoid splitting the vote, by reading between the lines somewhat we can identify most of the factors that will most likely have influenced the decision.