Solder will not attach to non-metallic surfaces. Therefore the component body need not be masked. On the other hand solder bridge between component pins is a definite possibility, which can only be alleviated by proper component layout or orientation.

Also as a general design rule try to place SMT ICs on the top side of the PCB so that it does not have to be soldered using wave process. If the design does not allow this then specialized fixtures or masking becomes necessary to avoid any bridging of the leads.

How thin is the flexible section? Can you support the area with FR4 material? This way you can create a pallet and mount via SMT machines.

Hand assembly using a stencil/paste will help and don't forget to bake first 2hrs @ 250 degrees.

The best way we've found to do that type of assembly is with fixturing to hold the flex in place, then paste it with solder paste, position the components and reflow in a preset profile oven.

The thing you want to do is hold the flex from moving during the paste deposition and component placement process. Once this is done, submit the entire assembly to the reflow process.

I would suggest that this is completed in a traditional SMT process with solder paste and an oven with blow speed control. The flex circuits are than placed into a "boat " fixture that carries them through the oven and allows for soldering. The boat is also used to keep the flex on a flat surface and at times used to hold the assembly.

Once the flex circuit material is secured, you can align the component by hand, apply liquid flux and using a hoof or mini-hoof soldering tip to hand solder the component in place.

The biggest concern you will have is overheating the flex material. I would suggest a Direct Power soldering iron with a 600 series tip cartridge. This combination will provide the speed that you need along with the low temperatures that will keep the assembly safe.

Using a Vapor Phase will provide an Oxygen free solder environment for best solder joint results. It will also guarantee 0 Deg delta T and provide a controlled ramp rate.

Vapor Phase systems are available as batch systems or in-line and so if this is a relatively low volume application, you could chose to run a batch system. This would save space and power when compared to a typical reflow oven.