if the IRS does not classify you as a dealer in real estate (the flip would be ordinary income and not capital gain), then short-term losses from stocks will offset the capital gain on the flip. long-term gains and losses are also netted. if one category is a loss and the other is a gain, these too are netted. the maximum deduction for capital losses in any one year is $3,000 with any excess carried over to the following year. if both are losses the short-term is used first.
see this guide about house flipping and you may want to consult a tax pro
https://www.realestateskills.com/blog/taxes-flipping-houses
