In the present case, we knew that collaboration would be a key theme, so we entered into the construction of this volume with the meta-issues not only in mind, but also in flux.
It's just the ordinary meaning of flux. I'd attribute the odd turn of phrase to zeugma.
flux noun 3 (mass noun) Continuous change. ‘since the fall of the wall Berlin has been a city in flux’ ‘the whole political system is in a state of flux’ - ODO
The quote says that because they knew the topic of collaboration was important, they started with the meta-issues in mind ... and because collaboration was important, they started with the assumption that the meta-issues weren't fixed. Presumably, the meta-issues would need to be sorted out via collaboration.