First off, thanks for asking this! Lesbians in AIDS work and the relationships between gay men and lesbians are probably my favorite things to talk about. This is a pretty open ended question, so I'm going to hit on a few different things.
Your question is about how lesbians were affected by HIV/AIDS. I'm going to look at two ways of understanding the word "affected."
Physically/medically, how were lesbians affected by HIV as a virus and AIDS as an illness?
Both the medical establishment and the lesbian community were unsure of the rates of HIV transmission in lesbian sex. The medical establishment was very much unconcerned with this as an issue. There was widespread ignorance of and indifference to lesbian sex in regards to health and medicine. The first case of woman-to-woman transmission confirmed by the CDC was confirmed only recently (sometime in the last two years, by my recollection.) I've come across quite a few examples in my research of women who insist that they were infected by a female partner. The medical establishment did exceedingly little to look into how AIDS affected lesbians (or women in general, more on that later.) Lesbian activists were very much focused on understanding their risks and adapting their sexual practices to compensate for those risks. Additionally, the medical establishment largely reduced the issue of AIDS among lesbians to the concept of woman-to-woman transmission. Lesbian activists were quick to point out how lesbian identity existed at the intersections: lesbians might be IV drug users, might be incarcerated, might be raped, and in some cases have consensual sex with male partners.
Just as the medical establishment was largely ignorant of how women and lesbians might contract HIV, they were equally ignorant of how AIDS affected the female body. AIDS is a syndrome caused by the collapse of the immune system. There are various opportunistic infections that are common to people with AIDS (PWA.) Until the early 1990's the CDC definition of AIDS was based off the kind of opportunistic infections found in gay men with AIDS. Women often experienced different infections. The threshold between being HIV-positive and having AIDS was (and more or less still is) a largely arbitrary one. In the eighties and early nineties an AIDS diagnosis was based on particular infections that signaled a substantial immune collapse. However, these particular infections were not alway found in women with AIDS. Huge numbers of women with AIDS were not being diagnosed. This not only meant that they were not being counted, it also meant that they were not eligible for disability benefits or for social services specifically for people with AIDS. Activists, notably ACT UP worked to change the CDC definition of AIDS to be more inclusive of women. The slogan they used was "Women don't get AIDS. They just die from it."
Socially, how were lesbians affected by AIDS as a political issue and cultural moment?
For much of the 1970's gay men and lesbians maintained largely separate political and social movements. This is not to say that there wasn't some shared activism and quite a few personal friendships between gay men and lesbians. AIDS brought gay men and lesbians together and integrated their movements in a way that had been largely absent for much of the 70's. Lesbians came to AIDS work for a variety of reasons. Sometimes they came to service work or activism because of their friendship with gay men, sometimes out of a shared gay identity and a fear of the increasing homophobia of the times, and sometimes out of a desire to do activist work.
Although gay men experienced the brunt of the public's AIDSphobia, lesbians did experience AIDS related homophobia. Lesbians, many of whom had been involved in lesbian health activism in the 1970's, were frustrated with the way women were cut out of AIDS treatment, research, and clinical trials. Many lesbians also felt conflicted about their involvement in AIDS work because they believed that few, if any, gay men would be involved in AIDS work if AIDS had been a issue primarily affecting lesbians. Although the lesbians involved in AIDS activism were deeply committed to their work, they were not infrequently frustrated by the misogyny of many gay men and the tendency of male-dominated AIDS activist groups to ignore issues of intersectionality.
Sources/further reading:
The Gravest Show on Earth by Elinor Burkett, particularly chapter seven, "Vaginal Politics"
How to Have Theory in an Epidemic by Paula A Treichler
Moving Politics by Deborah B. Gould
Also this little AMA I did a couple years ago may be of interest.