The answer to 2. is "yes" if we assume the graph has every edge contained in a cycle. First, observe that it suffices to prove it for rational weights - just subtract a tiny epsilon from each edge to make it's weight rational without altering the fact that each cycle has positive weight.
A weight function is $non-negative$ if the weight of any cycle is not negative. We claim that if $G$ has the property that every edge is contained in a cycle, then any non-negative rational weight function is flip equivalent to one where every edge has non-negative weight. Assume the claim is false. It suffices to prove the claim for integer weight functions by re-scaling. Pick a counterexample on a minimal number of vertices, and subject to that, to minimize $\sum_{e \in E(G)} w(e)$$\sum_{e \in E(G): w(e) \ge 0} w(e)$. If there exists a cycle $C$ such that $w(C) = 0$, then there exists a weight function $\bar{w}$ which is flip-equivalent to $w$ such that $\bar{w}(e) = 0$ for all edges $e \in E(C )$. To see this, number the edges of $C$ $e_1, \dots, e_k$ so that they occur in that order on $C$. We can force $e_i$ for $1 \le i \le k-1$ to have weight 0 by sequentially resigning on $\delta(v_{i+1})$. After doing so, the weight on $e_k$ will be the weight of the cycle, namely 0.
Consider the graph $G'$ obtained by contracting the cycle $C$ to a single vertex and deleting any loops which arise. Note that this preserves the property that every edge is contained in a cycle, and it also holds that each loop must have positive weight in $\bar{w}$. Let $w'$ be the weight function obtained by restricting $\bar{w}$ to the edges of $G'$. Then $G'$ has no negative weight circuit, since any such circuit could be rerouted through $C$ to give a negative weight cycle in $G$. Thus, $w'$ on $G'$ can be made non-negative by repeatedly resigning on cuts. Since each cut of $G'$ is a cut of $G$ as well, it follows that $\bar{w}$ can be made non-negative by repeatedly resigning on cuts.
Thus, we may assume that every cycle has strictly positive weight, and consequently, weight at least 1. It follows that there must exist an edge $f$ with $w(f) \ge 1$. Fix such an edge $f$, and let $w''$ be the weight function with $w''(e) = w(e)$ for all $e \neq f$ and let $w''(f) = w(f) - 1$. By construction, $w''$ is a non-negative since the weight of any cycle decreases by at most $1$. Moreover, $\sum_{e \in E(G)} w''(e)$$\sum_{e \in E(G): w''(e) \ge 0} w''(e)$ has strictly decreased, so by our choice of counterexample, there exists a weight function which is flip equivalent to $w''$ where every edge has non-negative weight. By resigning on the same series of cuts, we find a weight function which is flip equivalent to $w$ where every edge has non-negative weight, contradicting our choice of counterexample.