I am going to delete an entire subdomain which has been recognized by Google as a separate site for a long time but is closely linked to the main site. Will there be any SEO issues that I need to worry about or can I safely delete it?
You should have a VERY good reason to delete content from your site. The more pages you have on your site, the more chances you have to rank for more keywords, the more links you can attract, yada, yada, yada. That being said IF you insist on deleting an entire sub-domain of content, you should consider 301 redirecting requests for pages in that sub-domain back to your main domain. On a page by page basis, 301 redirect requests for each OLD URL on the sub-domain to a URL on your main domain whose content most closely resembles (from a topic/keyword perspective) the content of the page at the OLD URL. The reason you want to redirect those pages are many. The most important of which are: 1) If the sub-domain has been around a while then those old pages likely have inbound links from other websites, blogs, directories, etc. Inbound links are the MOST valuable asset your site has from an SEO perspective. The link text used to link to those pages have keywords in them that have the most influence on which keyword phrases your URLs rank for. They have the MOST influence on your rankings than any other one thing. By 301 redirecting the OLD URLs at the sub-domain to URLs on your main domain whose content most closely resembles the content of the OLD URL, the search engines will give your URLs on your main domain credit for those inbound links to the OLD URLs that will no longer exist after you shutdown the sub-domain. So you don't "waste" those links. At Google at least, they will also remove the OLD URLs from their index and replace them with the new URLs. 2) If you simply delete the pages on the sub-domain, you are going to break links on other sites. Users clicking on those links thinking they are going to your sub-domain are going to get a 404 error and likely guess that your site is now dead. 301 redirecting the OLD URLs on the sub-domain to your main domain gives those users an alternative. They likely won't even realize they've been sent to a different domain. NOTE: If you do NOT have a page on your main domain whose content is similar to that of one of your OLD URLs on the sub-domain then either 1) create a page on the main domain that is similar and 301 redirect to it or 2) allow the OLD URL to 404. You will want to leave the sub-domain live and the redirects in place indefinitely so that browsers and crawlers requesting the old pages can find the sub-domain to detect the 301 redirects. You can delete the pages once you have the redirects in place assuming you're NOT implementing the redirects inside your server-side scripts that generated the old pages on the sub-domain. If you're hosting your site on Apache, you have a host of powerful tools available to manage the redirects including Mod_Rewrite.
Yeah, I know what you're saying. There are two good reasons for deleting this content but they're both connected. It's basically a photo archive that has decent ranking but has not been updated for close to two years and receives too few hits to motivate keeping it in relation to its size. 301 redirects would be risky in this case I think and the visitors would be rather confused. There are naturally a few incoming links but they are generally rather worthless in comparison to those of the main site. Wouldn't the most natural and user friendly alternative in this case be to simply 404 all pages and offer the visitor an explanation and a link to the main site?
Like I said, if you don't have another page somewhere on your main domain with equivalent content and you don't want to build such a page then yes... the appropriate thing to do IS to 404. If your web server can be configured so that it has a custom 404 page for the sub-domain that is different from your main domain's custom 404 page, you can put specific wording on the sub-domain's 404 page that the Gallery no longer exists and provide links to the main domain that might be somewhat similar or of interest. If the two domains share the same custom 404 page, simply put a message on there that if you're looking for the gallery then it no longer exists. Sometimes it IS appropriate to simply 404... This sounds like such a situation.
The site is built on php and I can put an .htaccess in every single folder if I want to so that shouldn't be a problem. It seems like we're both thinking along the same lines on this topic, thanks for your input!