The utilization of NOL after merger or acquisition of corporations is complex and there are several restrictions by law.
As you mentioned, when the stock ownership changes by more than 50%, under section 382 of the Code, a corporation's income each year against which the NOLs can be applied after the acquisition is limited.
Under section 269 of the Code, if the primary purpose of a corporation acquiring another corporation's property is securing the benefit of tax attributes, including NOLs, it cannot use those tax attributes. If the acquiring company pays no more than a fair market price for the stock (not just the assets) of the acquired company in most cases this should satisfy the tax avoidance test. The parties involved should exercise caution to avoid the appearance that the tax benefit is a primary benefit of the transaction. The improved profitability and economics of purchasing the business should be the main reason and the tax beneift must be secondary to that reason.
Even if the restrictions under section 269 and section 382 are not applicable, when the acquired corporation continues as a separate corporation the consolidated return group rules mandate that post acquisition losses can be applied only against its own income and not against that of other members of the group. You need to consider what the future prospects are for each of the companies if operated separately.
When it applies, Code Section 384 flatly prohibits the use of a "pre- acquisition loss" (other than that of the gain corporation) to offset recognized built-in gains of a gain corporation during the recognition period. A "pre-acquisition loss" is any net operating loss (NOL) carryforward to the taxable year of acquisition, and any net operating loss incurred in that year to the extent it is attributable to a period before the acquisition date. For Code Section 384 to apply, the two following conditions must be met. First, there must be an acquisition (direct or indirect) of control of another corporation, and one of the corporations involved in the acquisition must be a "gain corporation." Code Section 384 does not apply if the loss corporation and the gain corporation were members of the same "controlled group" of corporations during the five years before the acquisition.
These types of reorganizations must be performed precisely in order to allow utilization of losses. You will need a tax attorney experienced in these matters. You will need to count the cost before making the decision.
You will also need to consider the state tax implications as the state treatment may or may not follow the federal treatment of the transaction. Please see this article State tax treatment of net operating loss carryovers in corporate acquisitions which also includes a review of the federal statutory scheme.
I hope that this general basic information on the use of NOL in corporate reorganizations is helpful as you confer with your professional advisors with all of the facts and circumstances.