Oftentimes open problems will have some evidence which leads to a prevailing opinion that a certain proposition, $P$, is true. However, more evidence is discovered, which might lead to a consensus that $\neg P$ is true. In both cases the evidence is not simply a "gut" feeling but is grounded in some heuristic justification.
Some examples that come to mind:
Because many decision problems, such as graph non-isomorphism, have nice probabilistic protocols, i.e. they are in $\mathsf{AM}$, but are not known to have certificates in $\mathsf{NP}$, a reasonable conjecture was that $\mathsf{NP}\subset\mathsf{AM}$. However, based on the conjectured existence of strong-enough pseudorandom number generators, a reasonable statement nowadays is that $\mathsf{NP}=\mathsf{AM}$, etc.
I learned from Andrew Booker that opinions of the number of solutions of $x^3+y^3+z^3=k$ with $(x,y,z)\in \mathbb{Z}^3$ have varied, especially after some heuristics from Heath-Brown. It is reasonable to state that most $k$ have an infinite number of solutions.
Numerical evidence suggests that for all $x$, $y$, we have $\pi(x+y)\leq \pi(x)+\pi(y)$. This is commonly known as the "second Hardy-Littlewood Conjecture". See also this MSF question. However, a 1974 paper showed that this conjecture is incompatible with the other, more likely first conjecture of Hardy and Littlewood.
- Number theory may also be littered with other such examples.
I'm interested if it has ever happened whether the process has ever repeated itself. That is:
Have there ever been situations wherein it is reasonable to suppose $P$, then, after some heuristic analysis, it is reasonable to supposed $\neg P$, then, after further consideration, it is reasonable to suppose $P$?
I have read that Cantor thought the Continuum Hypothesis is true, then he thought it was false, then he gave up.