I can't be absolutely sure, but this is the best explanation I can think of. First of all, the existing venting system must be less than optimal for this theory to apply. No one can confirm this for sure without significant (and likely destructive) investigation.
Second, the side line coming into the original "split" (tee-wye actually) is actually the vent for the basement toilet. The tee-wye was installed incorrectly for a vent due to constrictions of floor level and adjacent plumbing. The side inlet should have been rotated up 45 degrees for a proper vent take off. Improper vent take offs like this are quite common and do not always present any practical issues. It might even be allowed by some codes.
The horizontal line in the wall that drained into the former vent made it a wet vent. Depending on what the horizontal line is draining, the wet vent configuration is possibly an acceptable installation.
The new configuration where the vent take off is at the main drain stack from upstairs is incorrect. This makes a short section of the main drain a very much improper wet vent. Additionally, the horizontal section of new pipe now becomes a horizontal wet vent, which is not allowed by some codes, but might be by others.
The plumber apparently thought this vent was actually a drain, in which case the new installation would have been fine. But how did he think the toilet was vented?
This basement toilet vent is connected into the vents of other fixtures upstairs. This is completely normal. However, now that it is improperly tied into the main drain stack, falling waste water in the drain induces significant air pressure fluctuations in the vent pipe that never occurred with the old configuration. It is these pressure fluctuations in a pipe tied to the upstairs toilet vent(s?) causing your observed suction in the toilets.
Even though wrong, this configuration should not normally cause the problems you observe if the venting system were working correctly. There has to be some constriction in the vent path through the roof for the suction you see to be possible. Even though the most direct path from the roof down may be clear based on your testing, the actual toilet vent portion is still obstructed or misconfigured.
The solution to this problem is to properly vent the basement toilet and remove the tie in to the main drain stack. Venting the basement toilet properly is easier said than done due to a lot of plumbing happening in the immediate area. It's impossible to suggest an exact solution without much more information about how everything is laid out. It may be necessary to reconfigure the entire bathroom to get the toilet away from this congested area.
You will still have a venting issue upstairs, but at least this correction restores the original situation where suction was not a serious issue.