This is not likely a relationship between SMT glue and flux.

The SMT glue should be fully cured prior to any wave solder flux operations. Once cured the SMT glue is not likely to have any interaction with flux and serves no functional purpose after the wave solder process. The most likely scenario here is that the flux may not be active enough or not enough applied to the PCB to allow for cleaning of solder pads.

If the flux is not applied properly or is missing which is a common issue for Drum Fluxer type applicators then the molten solder will not wet to the pads and components. Components not properly soldered will fall off the PCB if the circuit board is flexed or bent as the SMT glue is not designed to be flexed.

You should verify if your current SMT glue is capable of handling the Lead Free Wave solder temperatures as this may be driving up your defect rates. Your flux may also have been designed for tin lead processes and not have enough activity for lead free processes.

There are several reasons why components may be missing off your PCB. Most of the occurrences of components falling off occur before the wave solder process. Some examples are below:

Dots to small or missing - effect is components coming before or during the wave solder process.

PCB Pad contamination - Contamination on PCB solder pads like grease or significant oxidation inhibiting solder wetting to reflow to pads during reflow process.

Excessive bending or flexing of circuit boards during manual component insertion prior to wave solder. Components may be coming off during this process prior to the wave solder process.

The glue or epoxy used to secure components which will be wave soldered must be able to withstand the thermal excursion and thermal shock of the wave solder process. Although the lead-free process uses a higher temperature than the tin/lead process epoxies should be selected accordingly.

I would suggest getting in touch with the epoxy supplier who can determine which of their products best meet your objectives. Depending upon where you are located your local supply representatives should be able to lead you in the right direction.

If the component is falling off after the wave solder process, I would investigate the cleanliness of the board prior to the application of the adhesive. As previously mentioned the adhesive should be able to withstand the process but it should also be able to adhere to either the laminate or the solder mask, and cleanliness of these elements is crucial to good adhesion.