I my past aquarium days I would have fish eggs hatch out in the aquariums and sucking them up with the cleaning siphon was a concern. I would use a hose as a siphon and suck only the fry out into a separate container and then clean the tank. Once the tank was clean I would pour the fry back in. This is assuming you can get the fry to move away from the debris so you can collect just the fry. I also set the siphon flow as low as possible so that the rapid water flow through the hose was less harsh on the fry, but would still suck up the fry.
I am afraid that the fry sucked up against your 90 micron mesh screen for any length of time might kill them.
I am assuming that you have debris on the bottom of the tank that needs to be cleaned out. If you are only doing partial water changes, I would suggest that you connect your siphon hose to the bottom of a bucket and then put your mesh over the top of the bucket. This will reduce the velocity of the water at the mess and reduce the likelihood of sucking fry up against the mesh.
