The short answer is maybe.
We need a few more details. The cleaning agent you are using is generally used in one of two ways; rinsed with water or simple solvent air dry. This is an important distinction for reasons I’ll explain later.
The cleaning agent is of course cleaning the soils on your stencils, that’s why you’re using it. With raw, un-reflowed solder paste as the cleaning agent does its job reacting with the paste, it free solder spheres, lead free or tin/lead into the solution. If the equipment employed does not have an effective filtration system, these solder spheres run a high, all but certain risk of being re-deposed onto any stencils cleaned in the machine. This is particularly true for those using the solvent air dry technique. If a water rinse is employed, these “loose” solder spheres should be rinsed off and not re-depose, but proving it would be a challenge.
Additionally, it is quite common for cleaning materials to absorb lead in stencil cleaning applications. After all, there is plenty of lead in raw paste, and while legacy technologies like the SC200 materials are not highly reactive the likelihood of absorbing some lead over an extended period of time is quite high. Once again, if you are employing the solvent air dry technique this absorbed lead will not evaporate and therefore will remain on your stencil. There is no where else for it to go. Once again, water rinsing should greatly alleviate this issue, but it may still be hard to prove.
Now let’s consider the water you are using to rinse. If it is virgin, DI water used once and flushed down the drain, there is little chance of lead being transferred to your lead free stencils. If you recycle the water, it once again comes down to whether you have proper filtration and maintain that filtration. These solder spheres are not very large, and can be challenge to remove with 100% certainty.
I have mentioned the possibility of some process effluent going down the drain. One of the advantages of the move to lead free is the tight regulation of lead throughout the world. In the USA, an effluent stream with 5 ppm lead is considered a hazardous waste and is highly regulated. Often local regulations for lead in waste water start at the 0.5 ppm level. The lab test to check for lead levels in a solution is quite inexpensive, under $50. As you are evaluating your system, these are always good test to run and have on hand for future audits.
So if you have solid filtration that is maintained well you are in pretty good shape. If you have a 10 year old machine allowing the solvent to air dry, consider upgrading your system and maybe the cleaning agent. Mature, legacy products like SC200 can still be effective, but there are modern lower cost of ownership alternatives available as well.
Hope this was helpful.