I've experienced loss of synchronization when editing/switching patches using Gearbox and X3L at the same time. I think you're right that it's best to use only Gearbox when it is running. Although as you say the X3L will respond to patch changes by pedal-pushing, it can then get out of sync. And things will almost certainly get out of sync if you edit/save a patch directly on the X3L and then edit it again using Gearbox. Very unpredictable behaviour in terms of what is actually being saved/stored on the X3L. For best results, don't touch the X3L manually while Gearbox is running.

As for the random effect/parameter changes I think you may be experiencing a completely different problem, depending on how old your X3L is. Older models have a known problem with footswitch failure, and even new units can experience 'float' in the associated knobs. A common symptom of both of these problems is exactly what you describe - random changes.

For the first issue - footswitch failure - search this forum under that topic. In some potst you will frind the exact serial number where the fix was intorduced into manufacturing. Models with earlier serial numbers are under a lifetime warranty for this issue. If yours qualifies, bring it in to the nearest autiohorized service centre for the free fix.

The second issue - float - is sometimes resolved by 'parking' the knobs at the min or max position. What happens is that very minor vibrations are being deteced by the X3L as a movement in the knob position, automatically turning the effect on or changing a parameter value. The knobs are much less sensitive to these fluctuations when the knob is at either end of the movement spectrum.

.... and make sure you don't have Tone 2 locked - that can cause an apparent loss/change in your expected Tone 2.

Hope this helps.