Sal,
Jax has a good point about utilizing your multi-profile oven and switching to a different profile. However, since some ovens cause trouble while cooling off and stabilizing, I will assume you do have to use the same profile for whatever reason.
I believe the answer is in your adhesive spec sheet about the damage such high temp may cause. The Loctite 36xx I used would be OK running through the reflow profile. Also, if you're reluctant to change the temperatures, you can still change the conveyor speed and have your adhesive cured. For this case, I don't think you need to check the spec sheet. The only function of the adhesive is keeping the components on the pads in the way they were placed. The higher conveyor speed might even help your cycle time assuming the boards fly through the chip shooters for the adhesive side.
I personally like running primary side first. I can use every possible support in the screen printer since there are no parts underneath yet. Then flip it over (assuming it's not a dense board where you'll have trouble finding spots for the support pins. This trouble also exists if you run secondary side first and can be minimized by preparing a template or determining coordinates for the support pin locations.) and place your chips on glue. There's no stress on the primary side components since a low temp profile will not cause any warpage. If you run the secondary side first, you might have some warpage which may cause vibration (and other) problems during placement.
So, there is more to consider other than "the impact of high temp to your adhesive" when you run the board at the same temps and speed for both sides.
The details of your application may still easily prove my concerns wrong.
Good Luck Erhan
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